diff --git a/spim_registration/timelapse/SingleChannel.yaml b/spim_registration/timelapse/SingleChannel.yaml
deleted file mode 100755
index 60b1688d0ca8bac5d1029846f28e22e181895169..0000000000000000000000000000000000000000
--- a/spim_registration/timelapse/SingleChannel.yaml
+++ /dev/null
@@ -1,189 +0,0 @@
-common: {
- # directory that contains the bean shell scripts
- bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
- directory_cuda: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/lib/",
- fiji-app: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/ImageJ-linux64",
- fiji-prefix: "/sw/bin/xvfb-run -a",
- first_xml_filename: "test_unicore",
- hdf5_xml_filename: '"hdf5_test_unicore"',
- merged_xml: "hdf5_test_unicore_merge",
- ntimepoints: 5,
- angles: "0,72,144,216,288",
- channels: "green",
- illumination: "0",
- pixel_distance_x: '0.28590106964',
- pixel_distance_y: '0.28590106964',
- pixel_distance_z: '1.50000',
- pixel_unit: "um",
- # transformation_switch: "timelapse_dublicate",
- transformation_switch: "timelapse",
- # fusion_switch: "deconvolution"
- fusion_switch: "fusion"
- }
-
-define_xml_czi: {
- first_czi: "2015-04-11_LZ2_Stock68_3.czi",
- rotation_around: "X-Axis",
- bsh_file: "define_czi.bsh"
- }
-
-define_xml_tif: {
- image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif',
- imglib_container: '"ArrayImg (faster)"',
- multiple_angles: '"YES (one file per angle)"',
- multiple_channels: '"NO (one channel)"',
- multiple_illumination_directions: '"NO (one illumination direction)"',
- multiple_timepoints: '"YES (one file per time-point)"',
- type_of_dataset: '"Image Stacks (ImageJ Opener)"',
- bsh_file: "define_tif_zip.bsh"
- }
-
-resave_hdf5: {
- hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"',
- resave_angle: '"All angles"',
- resave_channel: '"All channels"',
- resave_illumination: '"All illuminations"',
- resave_timepoint: '"All Timepoints"',
- setups_per_partition: '0',
- subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"',
- timepoints_per_partition: '1',
- bsh_file: "export.bsh"
- }
-
-registration: {
- # "Single Channel" is not a valid choice for "Process_channel"
- reg_process_channel: '"All channels"',
- reg_processing_channel: '"green"',
- reg_interest_points_channel: '"beads"',
- reg_radius_1: '2',
- reg_radius_2: '3',
- reg_threshold: '0.005',
- initial_sigma: '1.8',
- threshold_gaussian: '0.0080',
- type_of_detection: '"Difference-of-Mean (Integral image based)"',
- label_interest_points: '"beads"',
- reg_process_timepoint: '"Single Timepoint (Select from List)"',
- reg_process_angle: '"All angles"',
- reg_process_illumination: '"All illuminations"',
- subpixel_localization: '"3-dimensional quadratic fit"',
- detection_min_max: "find_maxima",
- type_of_registration: '"Register timepoints individually"',
- algorithm: '"Fast 3d geometric hashing (rotation invariant)"',
- transformation_model: "Affine",
- allowed_error_for_ransac: '5',
- significance: '10',
- fix_tiles: '"Fix first tile"',
- map_back_tiles: '"Map back to first tile using rigid model"',
- model_to_regularize_with: "Rigid",
- lambda: '0.10',
- imglib_container: '"ArrayImg (faster)"',
- bsh_file: "registration.bsh"
- }
-
-xml_merge: {
- bsh_file: "xml_merge.bsh"
- }
-
-timelapse: {
- reference_timepoint: '0',
- type_of_registration_timelapse: '"Match against one reference timepoint (no global optimization)"',
- timelapse_process_timepoints: '"All Timepoints"',
- bsh_file: "timelapse_registration.bsh"
- }
-
-Dublicate_transformations: {
- source_dublication: "red",
- target_dublication: "green",
- duplicate_which_transformations: '"Replace all transformations"',
- bsh_file: "Dublicate_transformations.bsh"
- }
-
-fusion: {
- bsh_file: "fusion.bsh",
- downsample: '4',
- fused_image: '"Append to current XML Project"',
- imglib2_container_fusion: '"ArrayImg"',
- imglib2_data_container: '"ArrayImg (faster)"',
- interpolation: '"Linear Interpolation"',
- minimal_x: '190',
- minimal_y: '-16',
- minimal_z: '-348',
- maximal_x: '1019',
- maximal_y: '1941',
- maximal_z: '486',
- pixel_type: '"16-bit unsigned integer"',
- process_angle: '"All angles"',
- process_channel: '"All channels"',
- process_illumination: '"All illuminations"',
- process_timepoint: '"Single Timepoint (Select from List)"',
- process_views_in_paralell: '"All"',
- xml_output: '"Save every XML with user-provided unique id"'
- }
-
-external_transform: {
- # channel setting: '"all_channels"'
- channel_setting: '"green"',
- transform_timepoint: '"All Timepoints"',
- transform_angle: '"All angles"',
- transform_channel: '"All channels"',
- # illumination setting only one illumination side
- transform_illumination: '"All illuminations"',
- apply_transformation: '"Current view transformations (appends to current transforms)"',
- define_mode_transform: '"Matrix"',
- matrix_transform: '"0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0"',
- transformation: '"Rigid"',
- bsh_file: "transform.bsh"
- }
-
-deconvolution: {
- iterations: '1',
- minimal_x_deco: '190',
- minimal_y_deco: '-16',
- minimal_z_deco: '-348',
- maximal_x_deco: '1019',
- maximal_y_deco: '1941',
- maximal_z_deco: '486',
- detections_to_extract_psf_for_channel: '"beads"',
- process_timepoint: '"Single Timepoint (Select from List)"',
- process_angle: '"All angles"',
- process_channel: '"All channels"',
- process_illumination: '"All illuminations"',
- Tikhonov_parameter: '0.0006',
- compute: '"in 512x512x512 blocks"',
- compute_on: '"GPU (Nvidia CUDA via JNA)"',
- imglib2_container: '"ArrayImg"',
- osem_acceleration: '"1 (balanced)"',
- psf_estimation: '"Extract from beads"',
- psf_size_x: '19',
- psf_size_y: '19',
- psf_size_z: '25',
- type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"',
- bsh_file: "deconvolution_GPU.bsh"
- }
-
-hdf5_output: {
- output_image_file_pattern: 'TP{{t}}_Chgreen_Ill0_Ang0,72,144,216,288.tif',
- output_xml: '"fused_Single_Channel"',
- output_hdf5_xml: '"hdf5_fused_Single_Channel"',
- output_multiple_channels: '"NO (one channel)"',
- output_timepoints: '0-4',
- output_pixel_distance_x: 0.5718,
- output_pixel_distance_y: 0.5718,
- output_pixel_distance_z: 0.5718,
- output_pixel_unit: 'um',
- output_channels: "green",
- output_data_type: "32Bit",
- convert_32bit: '"[Use min/max of first image (might saturate intenities over time)]"',
- output_type_of_dataset: '"Image Stacks (ImageJ Opener)"',
- output_multiple_timepoints: '"YES (one file per time-point)"',
- output_multiple_angles: '"NO (one angle)"',
- output_illumination_directions: '"NO (one illumination direction)"',
- output_imglib_container: '"ArrayImg (faster)"',
- subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}}, {{4,4,4}}, {{8,8,8}} }}"',
- chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}}, {{16,16,16}}, {{16,16,16}} }}"',
- # subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}} }}"',
- # chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}} }}"',
- bsh_file_define: "define_output.bsh",
- bsh_file_hdf5: "export_output.bsh"
- }
-
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 19798e53ed8258cb30911bdb4d00a557d41e85d2..f7211ce48505bc7396ac0bb0229d30df15118706 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -6,9 +6,13 @@ JOBDIR=os.path.abspath(os.path.curdir)
if JOBDIR[-1] != "/": # this checks if jobdir ends with slash if not it adds a slash
JOBDIR+="/"
-#data specific config file, expected to be inside JOBDIR
-# configfile: "tomancak_test_cluster.json"
-configfile: "tomancak_test_cluster.yaml"
+# Test config file single Channel:
+# configfile: "single_test.yaml"
+# Test config file dual channel one channel contains beads:
+configfile: "dual_OneChannel.yaml"
+
+# data specific config file, expected to be inside JOBDIR
+# configfile: "tomancak_test_cluster.yaml"
padding_format = "{0:0"+str(padding_of_file_id(int(config["common"]["ntimepoints"])))+"d}"
@@ -179,9 +183,15 @@ rule registration:
-Dreg_radius_1={reg_radius_1} \
-Dreg_radius_2={reg_radius_2} \
-Dreg_threshold={reg_threshold} \
- -Dinitial_sigma={initial_sigma} \
+ -Dsigma={sigma} \
-Dthreshold_gaussian={threshold_gaussian} \
- -Dregistration_algorithm={algorithm} \
+ -Dcompute_on={compute_on} \
+ -Ddirectory_cuda={directory_cuda} \
+ -Dseparableconvolution={separableconvolution} \
+ -Ddownsample_detection={downsample_detection} \
+ -Ddownsample_xy={downsample_xy} \
+ -Ddownsample_z={downsample_z} \
+ -Dregistration_algorithm={algorithm} \
-Dreg_interest_points_channel={reg_interest_points_channel} \
-Dfix_tiles={fix_tiles} \
-Dmap_back_tiles={map_back_tiles} \
@@ -254,10 +264,10 @@ rule timelapse:
cmd_string += " > {log} 2>&1 && touch {output}"
shell(cmd_string)
-rule dublicate_transformations:
+rule duplicate_transformations:
input: rules.timelapse.output, merged_xml="{xml_base}_merge.xml"
- output: rules.timelapse.output[0] + "_dublicate"
- log: "{xml_base}_dublicate_transformations.log"
+ output: rules.timelapse.output[0] + "_duplicate"
+ log: "{xml_base}_duplicate_transformations.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
@@ -296,7 +306,6 @@ rule fusion:
-Dprocess_illumination={process_illumination} \
-Dprocess_angle={process_angle} \
-Dxml_output={xml_output} \
- -Dfused_image={fused_image} \
-Dminimal_x={minimal_x} \
-Dminimal_y={minimal_y} \
-Dminimal_z={minimal_z} \
@@ -380,7 +389,9 @@ rule deconvolution:
-Dosem_acceleration={osem_acceleration} \
-DTikhonov_parameter={Tikhonov_parameter} \
-Dcompute={compute} \
- -Dpsf_estimation={psf_estimation} \
+ -Dcompute_on={compute_on} \
+ -Dcudafourierconvolution={cudafourierconvolution} \
+ -Dpsf_estimation={psf_estimation} \
-Ddirectory_cuda={directory_cuda} \
-Ddetections_to_extract_psf_for_channel={detections_to_extract_psf_for_channel} \
-Dpsf_size_x={psf_size_x} \
diff --git a/spim_registration/timelapse/cluster.json b/spim_registration/timelapse/cluster.json
index 4b2be746447e0fbd6c2b2892b30e26c895b4b0dd..7f13c62a6e51384d597d272137c18db3a2f97eb6 100755
--- a/spim_registration/timelapse/cluster.json
+++ b/spim_registration/timelapse/cluster.json
@@ -4,7 +4,12 @@
"lsf_extra" : "-R \"span[hosts=1]\"",
"lsf_q" : "short"
},
-
+
+ "resave_hdf5" :
+ {
+ "lsf_extra" : "-n 7 -R \"span[hosts=1] rusage[mem=50000]\""
+ },
+
"registration" :
{
"lsf_extra" : "-R \"span[hosts=1] rusage[mem=100000]\""
@@ -20,6 +25,11 @@
"lsf_extra" : "-R \"span[hosts=1] rusage[mem=10000]\""
},
+ "fusion" :
+ {
+ "lsf_extra" : "-n 12 -R \"span[hosts=1] rusage[mem=100000]\""
+ },
+
"deconvolution" :
{
"lsf_extra" : "-n 7 -R \"span[hosts=1] rusage[mem=50000]\"",
diff --git a/spim_registration/timelapse/deconvolution_GPU.bsh b/spim_registration/timelapse/deconvolution.bsh
similarity index 82%
rename from spim_registration/timelapse/deconvolution_GPU.bsh
rename to spim_registration/timelapse/deconvolution.bsh
index 32154c2c9986c8156073d169f1fa53071506cc35..1ecd9b960e59567c901217e65a0984533574d8b3 100755
--- a/spim_registration/timelapse/deconvolution_GPU.bsh
+++ b/spim_registration/timelapse/deconvolution.bsh
@@ -4,11 +4,11 @@ import ij.Prefs; // calls imagej settings
import java.lang.Runtime;
import java.io.File;
import java.io.FilenameFilter;
-
+
runtime = Runtime.getRuntime();
System.out.println(runtime.availableProcessors() + " cores available for multi-threading");
-Prefs.setThreads(7); // defines the number of threads allowed
+Prefs.setThreads(7); // defines the number of threads allowed
print("Threads: "+Prefs.getThreads()); // prints thread setting in output
System.out.println( "Start to load Parameters:" );
@@ -27,13 +27,12 @@ int parallel_timepoints = Integer.parseInt(System.getProperty( "parallel_timepoi
process_timepoint = System.getProperty( "process_timepoint" );
process_channel = System.getProperty( "process_channel" );
process_illumination = System.getProperty( "process_illumination" );
-process_angle = System.getProperty( "process_angle" );
-
+process_angle = System.getProperty( "process_angle" );
System.out.println( "-------------------------------------------------------" );
System.out.println( "General parameters: " );
System.out.println( "timepoint_processed = " + parallel_timepoints );
-System.out.println( "process_timepoints = " + process_timepoint );
+System.out.println( "process_timepoints = " + process_timepoint );
System.out.println( "process_channel = " + process_channel );
System.out.println( "process_illumination = " + process_illumination );
System.out.println( "process_angle = " + process_angle );
@@ -66,7 +65,6 @@ psf_estimation = System.getProperty( "psf_estimation" );
iterations = System.getProperty( "iterations" );
deco_output_file_directory = System.getProperty( "deco_output_file_directory" );
-
System.out.println( "-------------------------------------------------------" );
System.out.println( "Deconvolution settings: " );
System.out.println( "imglib2_container = " + imglib2_container_deco );
@@ -78,12 +76,6 @@ System.out.println( "psf_estimation = " + psf_estimation );
System.out.println( "number_of_iterations = " + iterations );
System.out.println( "deco_output_file_directory = " + deco_output_file_directory );
-// Search for CUDA
-System.out.println( "-------------------------------------------------------" );
-System.out.println( "Loading CUDA directory: " );
-directory_cuda = System.getProperty( "directory_cuda" );
-System.out.println( "directory_cuda = " + directory_cuda );
-
// PSF Parameters
psf_size_x = System.getProperty( "psf_size_x" );
psf_size_y = System.getProperty( "psf_size_y" );
@@ -101,24 +93,24 @@ System.out.println( "-------------------------------------------------------" );
System.out.println( "Channel Settings: " );
// Channel setting for Deconvolution
// parses channels and takes from there the number of channels
-// parses detections_to_extract_psf_for_channel
+// parses detections_to_extract_psf_for_channel
channels = System.getProperty( "channels" );
-System.out.println( "Channels = " + channels );
+System.out.println( "Channels = " + channels );
detections_to_extract_psf_for_channel = System.getProperty( "detections_to_extract_psf_for_channel" );
System.out.println( "PSF: " + detections_to_extract_psf_for_channel );
-// Splits channels and detections_to_extract_psf_for_channel
+// Splits channels and detections_to_extract_psf_for_channel
String delims = "[,]";
String[] channel_token = channels.split(delims);
String[] psf_token = detections_to_extract_psf_for_channel.split(delims);
-
-// Assembles channel_string
+
+// Assembles channel_string
StringBuilder channel_string = new StringBuilder();
for (int channel=0; channel < channel_token.length; channel++ )
-{
+{
String channel_part = "detections_to_extract_psf_for_channel_" + channel_token[channel] + "=" + psf_token[channel] + " ";
channel_string.append( channel_part );
channel_string.append(" ");
@@ -126,6 +118,45 @@ for (int channel=0; channel < channel_token.length; channel++ )
System.out.println( channel_string );
+// GPU/CPU setting
+System.out.println( "-------------------------------------------------------" );
+System.out.println( "GPU/CPU setting: " );
+
+compute_on = System.getProperty( "compute_on" );
+directory_cuda = System.getProperty( "directory_cuda" );
+cudafourierconvolution = System.getProperty( "cudafourierconvolution" );
+
+System.out.println( "compute_on = " + compute_on );
+System.out.println( "directory_cuda = " + directory_cuda );
+System.out.println( "cudafourierconvolution = " + cudafourierconvolution );
+
+String compute_string = "";
+String cuda_settings = "";
+
+if (compute_on.equalsIgnoreCase( "GPU (Nvidia CUDA via JNA)" ) )
+{
+ System.out.println( "GPU deconvoultion selected" );
+ compute_string = "compute_on=[GPU (Nvidia CUDA via JNA)] ";
+ cuda_settings = "cuda_directory=" + directory_cuda + " " +
+ "select_native_library_for_cudafourierconvolution=" + cudafourierconvolution + " " +
+ "gpu_1 ";
+}
+
+else if (compute_on.equalsIgnoreCase( "CPU (Java)" ) )
+{
+ System.out.println( "CPU deconvoultion selected" );
+ compute_string = "compute_on=[" + compute_on + "] ";
+ cuda_settings = "";
+}
+
+else
+{
+ System.out.println( "Deconvolution GPU/CPU selection bad" );
+}
+
+System.out.println( "compute_string=" + compute_string );
+System.out.println( "cuda_settings=" + cuda_settings );
+
// Execute Fiji Plugin
System.out.println( "=======================================================" );
System.out.println( "Starting Deconvolution" );
@@ -154,24 +185,21 @@ IJ.run("Fuse/Deconvolve Dataset",
"use_tikhonov_regularization " +
"tikhonov_parameter=" + Tikhonov_parameter + " " +
"compute=[" + compute + "] " +
- "compute_on=[GPU (Nvidia CUDA via JNA)] " +
+ compute_string +
"psf_estimation=[" + psf_estimation + "] " +
"psf_display=[Do not show PSFs] " +
"output_file_directory=" + deco_output_file_directory + " " +
- "cuda_directory=[" + directory_cuda + "] " +
- "select_native_library_for_cudafourierconvolution=libFourierConvolutionCUDALib.so " +
- "gpu_1 " +
+ cuda_settings +
channel_string +
"psf_size_x=" + psf_size_x + " " +
"psf_size_y=" + psf_size_y + " " +
"psf_size_z=" + psf_size_z + "");
}
-catch ( e ) {
+catch ( e ) {
print( "[deconvolution-GPU] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
-
}
/* shutdown */
diff --git a/spim_registration/timelapse/define_czi.bsh b/spim_registration/timelapse/define_czi.bsh
index e3e1d30e788e27aa6888ce5a4a7e352162aae4d5..aa6b0526148588817ababb68666eacb6e7529e3e 100755
--- a/spim_registration/timelapse/define_czi.bsh
+++ b/spim_registration/timelapse/define_czi.bsh
@@ -48,7 +48,6 @@ String angle_part;
angle_part = "angle_" + num_angles + "=" + angle_token[angle];
angle_string.append(angle_part);
angle_string.append(" ");
-
}
System.out.println( angle_string );
@@ -76,9 +75,7 @@ String channel_part;
channel_part = "channel_" + num_channel + "=" + channel_token[channel];
channel_string.append(channel_part);
channel_string.append(" ");
-
}
-
System.out.println( "Channel String = " + channel_string );
System.out.println("---------------------------------------------------------");
@@ -104,7 +101,6 @@ String illum_part;
illum_part = "_______illumination_" + num_illum + "=" + illum_token[illum];
illum_string.append(illum_part);
illum_string.append(" ");
-
}
System.out.println( illum_string );
diff --git a/spim_registration/timelapse/dual_OneChannel.yaml b/spim_registration/timelapse/dual_OneChannel.yaml
new file mode 100755
index 0000000000000000000000000000000000000000..239f9dfd3b117367df8297cf56f13414c695f349
--- /dev/null
+++ b/spim_registration/timelapse/dual_OneChannel.yaml
@@ -0,0 +1,260 @@
+common: {
+ # directory that contains the bean shell scripts and Snakefile
+ bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
+ # Directory that contains the cuda libraries
+ directory_cuda: "/sw/users/schmied/cuda/",
+ # Directory that contains the current working Fiji
+ #fiji-app: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/ImageJ-linux64",
+ fiji-app: "/sw/users/schmied/packages/2015-05-29_Fiji_2.3.9_SNAP.app.cuda/ImageJ-linux64",
+ fiji-prefix: "/sw/bin/xvfb-run -a", # calls xvfb for Fiji headless mode
+ # xml file names without .xml suffix
+ first_xml_filename: "Dual_Channel", # Name of the xml file for the .czi or .tif files
+ hdf5_xml_filename: '"hdf5_Dual_Channel"', # Name of .xml file for the hdf5 data after resave_hdf5
+ merged_xml: "hdf5_Dual_Channel_merge", # Name of .xml file after merge
+ # Describe the dataset
+ ntimepoints: 2, # number of timepoints of dataset
+ angles: "0,72,144,216,288", # angles
+ channels: "green,red", # channels
+ illumination: "0", # illuminations
+ pixel_distance_x: '0.28590', # Manual calibration x
+ pixel_distance_y: '0.28590', # Manual calibration y
+ pixel_distance_z: '1.50000', # Manual calibration z
+ pixel_unit: "um", # unit of manual calibration
+ # Use switches to decide which processing steps you need:
+ # transformation_switch: "timelapse" standard processing
+ # after timelapse registration directly goes into fusion, timelapse_duplicate
+ # "timelapse_duplicate" for dual channel processing one channel contains the beads
+ # duplicates transformations
+ transformation_switch: "timelapse_duplicate",
+ # Switches between content based fusion and deconvoltion
+ # "deconvolution" > for deconvolution
+ # "fusion" > for content based fusion
+ fusion_switch: "fusion"
+ }
+
+define_xml_czi: {
+ first_czi: "2015-02-20_LZ2_Stock48_Stock58.czi", # master .czi file
+ rotation_around: "X-Axis", # axis of acquistion
+ bsh_file: "define_czi.bsh" # .bsh script for defining .czi file
+ }
+
+define_xml_tif: {
+ # file pattern of .tif files
+ # for multi channel give spim_TL{tt}_Angle{a}_Channel{c}.tif
+ # # SPIM file pattern: for padded zeros use tt
+ image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif',
+ # Settings for ImageJ Opener
+ type_of_dataset: '"Image Stacks (ImageJ Opener)"',
+ multiple_timepoints: '"YES (one file per time-point)"', # or NO (one time-point)
+ multiple_angles: '"YES (one file per angle)"', # or NO (one angle)
+ multiple_channels: '"NO (one channel)"', # or "\"NO (one channel)\""
+ multiple_illumination_directions: '"NO (one illumination direction)"', # or YES (one file per illumination direction)
+ imglib_container: '"ArrayImg (faster)"', # '"ArrayImg (faster)"'
+ bsh_file: "define_tif_zip.bsh"
+ }
+
+resave_hdf5: {
+ # Resaves .tif or .czi data into hdf5
+ # Subsampling and resolution settings for hdf5: data dependent
+ hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"',
+ subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"',
+ # Standard settings for cluster processing
+ setups_per_partition: '0',
+ timepoints_per_partition: '1',
+ resave_timepoint: '"All Timepoints"',
+ resave_angle: '"All angles"',
+ resave_channel: '"All channels"',
+ resave_illumination: '"All illuminations"',
+ bsh_file: "export.bsh"
+ }
+
+registration: {
+ # reg_process_channel:
+ # # Single Channel: '"All channels"'
+ # Dual Channel: '"All channels"'
+ # Dual Channel one Channel contains beads: '"Single channel (Select from List)"'
+ reg_process_channel: '"Single channel (Select from List)"',
+ # reg_processing_channel:
+ # Dual Channel setting for 1 Channel contains the beads
+ reg_processing_channel: '"red"',
+ # reg_interest_points_channel:
+ # Single Channel: '"beads"'
+ # Dual Channel: '"beads,beads"'
+ # Dual Channel: Channel does not contain the beads '"[DO NOT register this channel],beads"'
+ reg_interest_points_channel: '"beads"',
+ # type of detection: '"Difference-of-Mean (Integral image based)"' or '"Difference-of-Gaussian"'
+ type_of_detection: '"Difference-of-Mean (Integral image based)"',
+ # Settings for Difference-of-Mean
+ # For multiple channels 'value1,value2' delimiter is ,
+ reg_radius_1: '2',
+ reg_radius_2: '3',
+ reg_threshold: '0.005',
+ # Settings for Difference-of-Gaussian
+ # For multiple channels 'value1,value2' delimiter is ,
+ sigma: '1.8',
+ threshold_gaussian: '0.0080',
+ # Processing setting for Difference-of-Gaussian detection
+ # compute_on:
+ compute_on: '"GPU accurate (Nvidia CUDA via JNA)"',
+ separableconvolution: '"libSeparableConvolutionCUDALib.so"',
+ # Downsampling settings
+ downsample_detection: "No", # "No" or "Yes"
+ downsample_xy: '"Match Z Resolution (less downsampling)"',
+ downsample_z: "1x",
+ # Standard Settings for bead based registration
+ label_interest_points: '"beads"',
+ reg_process_timepoint: '"Single Timepoint (Select from List)"',
+ reg_process_angle: '"All angles"',
+ reg_process_illumination: '"All illuminations"',
+ subpixel_localization: '"3-dimensional quadratic fit"',
+ detection_min_max: "find_maxima",
+ type_of_registration: '"Register timepoints individually"',
+ algorithm: '"Fast 3d geometric hashing (rotation invariant)"',
+ transformation_model: "Affine",
+ allowed_error_for_ransac: '5',
+ significance: '10',
+ fix_tiles: '"Fix first tile"',
+ map_back_tiles: '"Map back to first tile using rigid model"',
+ model_to_regularize_with: "Rigid",
+ lambda: '0.10',
+ imglib_container: '"ArrayImg (faster)"',
+ bsh_file: "registration.bsh" # .bsh script for registration
+ }
+
+xml_merge: {
+ bsh_file: "xml_merge.bsh"
+ }
+
+timelapse: {
+ reference_timepoint: '0', # Reference timepoint
+ # Standard settings for timelapse registration
+ type_of_registration_timelapse: '"Match against one reference timepoint (no global optimization)"',
+ timelapse_process_timepoints: '"All Timepoints"',
+ bsh_file: "timelapse_registration.bsh"
+ }
+
+dublicate_transformations: {
+ # If dual channel processing and only one channel contains beads
+ # this allows you to dublicate the transformation for the
+ # channel that does not contain beas
+ source_dublication: "red", # source channel
+ target_dublication: "green", # target channel
+ duplicate_which_transformations: '"Replace all transformations"', # mode of dublication
+ bsh_file: "dublicate_transformations.bsh" # .bsh script for dublication
+ }
+
+fusion: {
+ # content based multiview fusion
+ # supports multi channel without new settings
+ downsample: '1', # set downsampling
+ # Cropping parameters of full resolution
+ minimal_x: '220',
+ minimal_y: '40',
+ minimal_z: '-290',
+ maximal_x: '976',
+ maximal_y: '1892',
+ maximal_z: '472',
+ # fused_image: '"Append to current XML Project"', does not work yet
+ process_timepoint: '"Single Timepoint (Select from List)"',
+ process_angle: '"All angles"',
+ process_channel: '"All channels"',
+ process_illumination: '"All illuminations"',
+ imglib2_container_fusion: '"ArrayImg"',
+ interpolation: '"Linear Interpolation"',
+ pixel_type: '"16-bit unsigned integer"',
+ imglib2_data_container: '"ArrayImg (faster)"',
+ process_views_in_paralell: '"All"',
+ xml_output: '"Save every XML with user-provided unique id"',
+ bsh_file: "fusion.bsh"
+ }
+
+external_transform: {
+ # Downsamples for deconvolution
+ # BUG: external transformation breaks .xml file
+ # channel setting: '"all_channels"'
+ channel_setting: '"green,red"',
+ transform_timepoint: '"All Timepoints"',
+ transform_angle: '"All angles"',
+ transform_channel: '"All channels"',
+ transform_illumination: '"All illuminations"',
+ apply_transformation: '"Current view transformations (appends to current transforms)"',
+ define_mode_transform: '"Matrix"',
+ # Matrix for downsampling
+ matrix_transform: '"0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0"',
+ transformation: '"Rigid"',
+ bsh_file: "transform.bsh"
+ }
+
+deconvolution: {
+ iterations: '1', # number of iterations
+ # Cropping parameters: take downsampling into account
+ minimal_x_deco: '190',
+ minimal_y_deco: '-16',
+ minimal_z_deco: '-348',
+ maximal_x_deco: '1019',
+ maximal_y_deco: '1941',
+ maximal_z_deco: '486',
+ # Channel settings for deconvolution
+ # Single Channel: '"beads"'
+ # Dual Channel: '"beads,beads"'
+ # Dual Channel one channel contains beads: '"[Same PSF as channel red],beads"'
+ detections_to_extract_psf_for_channel: '"[Same PSF as channel red],beads"',
+ # Settings for GPU or CPU processing
+ # '"CPU (Java)"' or '"GPU (Nvidia CUDA via JNA)"'
+ compute_on: '"GPU (Nvidia CUDA via JNA)"',
+ cudafourierconvolution: "libFourierConvolutionCUDALib.so", # GPU processing name of cuda library
+ # Standard settings for deconvolution
+ process_timepoint: '"Single Timepoint (Select from List)"',
+ process_angle: '"All angles"',
+ process_channel: '"All channels"',
+ process_illumination: '"All illuminations"',
+ type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"',
+ Tikhonov_parameter: '0.0006',
+ compute: '"in 512x512x512 blocks"',
+ osem_acceleration: '"1 (balanced)"',
+ psf_estimation: '"Extract from beads"',
+ psf_size_x: '19',
+ psf_size_y: '19',
+ psf_size_z: '25',
+ imglib2_container: '"ArrayImg"',
+ bsh_file: "deconvolution.bsh"
+ }
+
+hdf5_output: {
+ # writes new hdf5 dataset for fusion output: will be obsolete
+ # Naming pattern of output
+ # Single Channel: TP{t}_Chgreen_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
+ # Dual Channel: TP{t}_Ch{0}_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
+ output_image_file_pattern: 'TP{{t}}_Ch{{c}}_Ill0_Ang0,72,144,216,288.tif',
+ # channel setting
+ output_multiple_channels: '"YES (one file per channel)"', # '"YES (one file per channel)"' or '"NO (one channel)"'
+ output_channels: "green,red",
+ # .xml file names
+ output_xml: '"fused_Dual_Channel"',
+ output_hdf5_xml: '"hdf5_fused_Dual_Channel"',
+ output_timepoints: '0-1', # Timepoints format: '1-2'
+ # pixel size of output: take downsampling into account!
+ output_pixel_distance_x: 0.28590,
+ output_pixel_distance_y: 0.28590,
+ output_pixel_distance_z: 0.28590,
+ output_pixel_unit: 'um',
+ # give if 16Bit data or 32Bit data
+ # output of fusion is 16Bit, of deconvolution it is 32Bit
+ output_data_type: "16Bit", # "32Bit" or "16Bit"
+ # if data is 32Bit then the data is converted into 16Bit data
+ convert_32bit: '"[Use min/max of first image (might saturate intenities over time)]"',
+ # subsampling and chunk size settings: dataset dependent
+ subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}}, {{4,4,4}}, {{8,8,8}} }}"', # data dependent
+ chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}}, {{16,16,16}}, {{16,16,16}} }}"', # data dependent
+ # subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}} }}"',
+ # chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}} }}"',
+ # Standard settings for hdf5_output
+ output_type_of_dataset: '"Image Stacks (ImageJ Opener)"',
+ output_multiple_timepoints: '"YES (one file per time-point)"',
+ output_multiple_angles: '"NO (one angle)"',
+ output_illumination_directions: '"NO (one illumination direction)"',
+ output_imglib_container: '"ArrayImg (faster)"',
+ bsh_file_define: "define_output.bsh", # .bsh script for defining the dataset
+ bsh_file_hdf5: "export_output.bsh" # .bsh script for resaving into hdf5
+ }
+
diff --git a/spim_registration/timelapse/registration.bsh b/spim_registration/timelapse/registration.bsh
old mode 100755
new mode 100644
index d6872232b191687a082c3e8f591979528318672e..31140723327eb85b805aa9219871608efce85aa8
--- a/spim_registration/timelapse/registration.bsh
+++ b/spim_registration/timelapse/registration.bsh
@@ -10,7 +10,7 @@ import java.lang.Object;
runtime = Runtime.getRuntime();
System.out.println(runtime.availableProcessors() + " cores available for multi-threading");
-//Prefs.setThreads(1); // defines the number of threads allowed
+//Prefs.setThreads(1); // defines the number of threads allowed
//print("Threads: "+Prefs.getThreads()); // prints thread setting in output
System.out.println("Start loading parameters");
@@ -32,10 +32,10 @@ int parallel_timepoints = Integer.parseInt(System.getProperty( "parallel_timepoi
unique_id = System.getProperty( "parallel_timepoints" );
reg_process_timepoint = System.getProperty( "reg_process_timepoint" );
reg_process_illumination = System.getProperty( "reg_process_illumination" );
-reg_process_angle = System.getProperty( "reg_process_angle" );
+reg_process_angle = System.getProperty( "reg_process_angle" );
System.out.println( "parallel_timepoints = " + parallel_timepoints );
-System.out.println( "process_timepoints = " + reg_process_timepoint );
+System.out.println( "process_timepoints = " + reg_process_timepoint );
System.out.println( "process_illumination = " + reg_process_illumination );
System.out.println( "process_angle = " + reg_process_angle );
@@ -81,6 +81,37 @@ System.out.println( "significance = " + significance );
// detection_min_max = System.getProperty( "detection_min_max" );
// System.out.println( "detection_min_max = " + detection_min_max );
+
+System.out.println( "-------------------------------------------------------" );
+System.out.println( "Downsampling: " );
+
+downsample_detection = System.getProperty( "downsample_detection" );
+downsample_xy = System.getProperty( "downsample_xy" );
+downsample_z = System.getProperty( "downsample_z" );
+
+System.out.println( "downsample_detection = " + downsample_detection );
+System.out.println( "downsample_xy = " + downsample_xy );
+System.out.println( "downsample_z = " + downsample_z );
+
+// downsample switch
+if (downsample_detection.equalsIgnoreCase("Yes") )
+{
+ System.out.println( "Downsampling is turned on" );
+ downsample_string = "downsample_xy=[" + downsample_xy + "] " +
+ "downsample_z=" + downsample_z + " ";
+}
+
+else if (downsample_detection.equalsIgnoreCase("No") )
+{
+ System.out.println( "Downsampling is turned off" );
+ downsample_string = "";
+}
+
+else
+{
+ System.out.println("Warning: Downsample setting bad");
+}
+
System.out.println( "-------------------------------------------------------" );
System.out.println( "Channel setting for Detection: " );
@@ -91,108 +122,221 @@ System.out.println( "Channel setting for Detection: " );
// from this it decides which string to assemble
reg_process_channel = System.getProperty( "reg_process_channel" );
System.out.println( "process_channel = " + reg_process_channel );
-
-reg_processing_channel = System.getProperty( "reg_processing_channel" );
-System.out.println( "processing_channel = channel " + reg_processing_channel );
-
+reg_processing_channel = System.getProperty( "reg_processing_channel" );
+System.out.println( "processing_channel = channel " + reg_processing_channel );
channels = System.getProperty( "channels" );
System.out.println( "Channels = " + channels );
+// Difference of Mean Settings
reg_radius_1 = System.getProperty( "reg_radius_1" );
System.out.println( "reg_radius_1 = " + reg_radius_1 );
-
reg_radius_2 = System.getProperty( "reg_radius_2" );
System.out.println( "reg_radius_2 = " + reg_radius_2 );
-
reg_threshold = System.getProperty( "reg_threshold" );
-System.out.println( "reg_threshold = " + reg_threshold);
-
-// Splits up channels, reg_radius_1, reg_radius_2 and reg_threshold
+System.out.println( "reg_threshold = " + reg_threshold);
+
+// Difference of Gaussian Settings
+sigma = System.getProperty( "sigma" );
+threshold_gaussian = System.getProperty( "threshold_gaussian" );
+compute_on = System.getProperty( "compute_on");
+directory_cuda = System.getProperty( "directory_cuda" );
+separableconvolution = System.getProperty( "separableconvolution" );
+
+System.out.println( "sigma = " + sigma );
+System.out.println( "threshold = " + threshold_gaussian );
+System.out.println( "compute_on = " + compute_on );
+System.out.println( "directory_cuda = " + directory_cuda );
+System.out.println( "separableconvolution = " + separableconvolution );
+
+// Sets delimiter
String delims = "[,]";
+
+// parses channels
String[] channel_token = channels.split(delims);
+
+// parses settings for Difference of Mean
String[] radius_1_token = reg_radius_1.split(delims);
String[] radius_2_token = reg_radius_2.split(delims);
String[] threshold_token = reg_threshold.split(delims);
+// parses settings for Difference of Gaussian
+String[] sigma_token = sigma .split(delims);
+String[] dog_threshold_token = threshold_gaussian.split(delims);
+
+// Defines variables for compute_string and sets it to an empty string
+String compute_string = "";
+
+// Defines variables for channel_string and sets it to an empty string
String channel_string = "";
+
+// Defines variables for processing_channel_string and sets it to an empty string
String processing_channel_string = "";
+
+// Defines variables for channel_string_multi and activates StringBuilder
StringBuilder channel_string_multi = new StringBuilder();
-
+
// If there are no channels set returns an error
if (channels.equalsIgnoreCase(""))
{
System.out.println("Warning: There are no channels set");
}
-
-// Returns an Error if there is one channel in channels but multiple settings in radius and or threshold
+
+// Returns an Error if there is one channel in channels but multiple settings in radius and or threshold
else if ( channel_token.length == 1 && (radius_1_token.length > 1 || radius_2_token.length > 1 || threshold_token.length > 1 ) )
{
System.out.println( "Error: Only one channel detected but multiple channel settings for radius or threshold" );
}
-
-// Assembles String for Singel Channel
-else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length == 1 )
+
+// Assembles String for Singel Channel
+else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length == 1 )
{
+ System.out.println( "Channel Setting: Multiple channels" );
processing_channel_string = "";
- channel_string_multi.append("");
- channel_string = "interest_point_specification=[Advanced ...] " +
- "radius_1=" + reg_radius_1 + " " +
- "radius_2=" + reg_radius_2 + " " +
- "threshold=" + reg_threshold + " " +
- "find_maxima";
-}
-
+ channel_string_multi.append("");
+// Switches between Difference-of-Mean and Difference-of-Gaussian Settings
+ if (type_of_detection.equalsIgnoreCase( "Difference-of-Mean (Integral image based)" ) )
+ {
+ channel_string = "interest_point_specification=[Advanced ...] " +
+ "radius_1=" + reg_radius_1 + " " +
+ "radius_2=" + reg_radius_2 + " " +
+ "threshold=" + reg_threshold + " " +
+ "find_maxima";
+ }
+
+ else if (type_of_detection.equalsIgnoreCase( "Difference-of-Gaussian" ) )
+ {
+ channel_string = "interest_point_specification=[Advanced ...] " +
+ "sigma=" + sigma + " " +
+ "threshold=" + threshold_gaussian + " " +
+ "find_maxima ";
+ }
+
+ else
+ {
+ System.out.println( "Error: type_of_detection selection is bad" );
+ }
+}
+
// Dual Channels both Channels contain beads
else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length > 1 )
{
- // Assembles String using StringBuilder for 2 Channels
- for (int channel=0; channel < channel_token.length; channel++ )
+ System.out.println( "Channel Setting: Multiple channels" );
+
+ // Assembles String using StringBuilder for 2 Channels
+ // Switches between Difference-of-Mean and Difference-of-Gaussian Settings
+ if (type_of_detection.equalsIgnoreCase( "Difference-of-Mean (Integral image based)" ) )
+ {
+ for (int channel=0; channel < channel_token.length; channel++ )
+ {
+ String channel_part = "interest_point_specification_(channel_" + channel_token[channel] + ")=[Advanced ...] " +
+ "radius_1_" + channel_token[channel] + "=" + radius_1_token[channel] + " " +
+ "radius_2_" + channel_token[channel] + "=" + radius_2_token[channel] + " " +
+ "threshold_" + channel_token[channel] + "=" + threshold_token[channel] + " " +
+ "find_maxima_" + channel_token[channel];
+ channel_string_multi.append(channel_part);
+ channel_string_multi.append(" ");
+ }
+ }
+
+ else if (type_of_detection.equalsIgnoreCase( "Difference-of-Gaussian" ) )
+ {
+ for (int channel=0; channel < channel_token.length; channel++ )
+ {
+
+ String channel_part = "interest_point_specification_(channel_" + channel_token[channel] + ")=[Advanced ...] " +
+ "sigma_" + channel_token[channel] + "=" + sigma_token[channel] + " " +
+ "threshold_" + channel_token[channel] + "=" + dog_threshold_token[channel] + " " +
+ "find_maxima_" + channel_token[channel] + " ";
+ channel_string_multi.append(channel_part);
+ channel_string_multi.append(" ");
+ }
+ }
+
+ else
{
- String channel_part = "interest_point_specification_(channel_" + channel_token[channel] + ")=[Advanced ...] " +
- "radius_1_" + channel_token[channel] + "=" + radius_1_token[channel] + " " +
- "radius_2_" + channel_token[channel] + "=" + radius_2_token[channel] + " " +
- "threshold_" + channel_token[channel] + "=" + threshold_token[channel] + " " +
- "find_maxima_" + channel_token[channel];
- channel_string_multi.append(channel_part);
- channel_string_multi.append(" ");
+ System.out.println( "Error: type_of_detection selection is bad" );
}
}
-
+
// Returns an Error if set to Dual Channel one Channel contains beads but there is only one channel in channels
else if ( reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && channel_token.length == 1 )
{
System.out.println( "Error: reg_process_channel or channels set incorrectly" );
}
-
+
// Returns and Error if set to Dual Channel processing one channel contains the beads but there are multiple settings in radius and or threshold
else if ( reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && (radius_1_token.length > 1 || radius_2_token.length > 1 || threshold_token.length > 1 ) )
{
- System.out.println( "Error: You said you wanted to process only one channel but there are multiple settings for radius or threshold" );
-}
-
+ System.out.println( "Error: Set to process only one channel but multiple settings for radius or threshold" );
+}
+
// Assembles String for Dual Channel but only one Channel contains beads
-else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && channel_token.length > 1)
-{
- channel_string_multi.append("");
- processing_channel_string = "processing_channel=[channel " + reg_processing_channel + "] ";
- channel_string = "interest_point_specification=[Advanced ...] " +
- "radius_1=" + reg_radius_1 + " " +
- "radius_2=" + reg_radius_2 + " " +
- "threshold=" + reg_threshold + " " +
- "find_maxima";
+else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && channel_token.length > 1)
+{
+
+ System.out.println( "Channel Setting: Multiple channels one channel contains beads" );
+ // Switches between Difference-of-Mean and Difference-of-Gaussian Settings
+ if (type_of_detection.equalsIgnoreCase( "Difference-of-Mean (Integral image based)" ) )
+ {
+ channel_string_multi.append("");
+ processing_channel_string = "processing_channel=[channel " + reg_processing_channel + "] ";
+ channel_string = "interest_point_specification=[Advanced ...] " +
+ "radius_1=" + reg_radius_1 + " " +
+ "radius_2=" + reg_radius_2 + " " +
+ "threshold=" + reg_threshold + " " +
+ "find_maxima";
+ }
+
+ else if (type_of_detection.equalsIgnoreCase( "Difference-of-Gaussian" ) )
+ {
+ channel_string_multi.append("");
+ processing_channel_string = "processing_channel=[channel " + reg_processing_channel + "] ";
+ channel_string = "interest_point_specification=[Advanced ...] " +
+ "sigma=" + sigma + " " +
+ "threshold=" + threshold_gaussian + " " +
+ "find_maxima ";
+ }
}
// Returns and Error if no conditions above are met
else
{
- System.out.println( "Error: Incorrect settings" );
+ System.out.println( "Error: Incorrect Detection of Interest points settings" );
}
-
+
+// Compute on settings for Difference-of-Gaussian
+if (type_of_detection.equalsIgnoreCase( "Difference-of-Mean (Integral image based)" ) )
+{
+ System.out.println( "Bead detection set to Difference-of-Mean (Integral image based)" );
+ compute_string = "";
+}
+
+else if (type_of_detection.equalsIgnoreCase( "Difference-of-Gaussian" ) && compute_on.equalsIgnoreCase( "CPU (Java)" ) )
+{
+ System.out.println( "Bead detection set to Difference-of-Gaussian processing on CPU" );
+ compute_string = "compute_on=[" + compute_on + "]";
+}
+
+else if (type_of_detection.equalsIgnoreCase( "Difference-of-Gaussian" ) && ( compute_on.equalsIgnoreCase( "GPU accurate (Nvidia CUDA via JNA)" ) ) ) // need second setting
+{
+ System.out.println( "Bead detection set to Difference-of-Gaussian processing on GPU" );
+ compute_string = "compute_on=[" + compute_on + "] " +
+ "directory_cuda=" + directory_cuda + " " +
+ "select_native_library_for_cudaseparableconvolution=" +separableconvolution;
+}
+
+else
+{
+ System.out.println( "Settings for [Difference of Gaussian:compute on] is bad" );
+}
+
+System.out.println( "downsample = " + downsample_string );
System.out.println( "Processing Channel = " + processing_channel_string );
System.out.println( "Channel String: " + channel_string );
System.out.println( reg_process_channel );
System.out.println( "Multi channel String: " + channel_string_multi );
+System.out.println( "Compute on=" + compute_string );
// Channel Setting Registration
System.out.println( "-------------------------------------------------------" );
@@ -212,31 +356,31 @@ System.out.println( "reg_interest_points_channel = " + reg_interest_points_chann
String[] interest_token = reg_interest_points_channel.split(delims);
String reg_single_channel_string ="";
StringBuilder reg_multi_channel_string = new StringBuilder();
-
+
// If there are no channels set returns an error
if (channels.equalsIgnoreCase(""))
{
System.out.println("Warning: There are no channels set");
}
-
+
// Assembles string for Single Channel registration
-else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length == 1 && interest_token.length == 1 )
-{
+else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length == 1 && interest_token.length == 1 )
+{
reg_multi_channel_string.append( "" );
reg_single_channel_string = "interest_points_channel_" + channels + "=" + reg_interest_points_channel + " ";
}
-
+
// Returns error if Multi Channels are selected but not enough settings in channels or reg_interest_points_channel
-else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && ( channel_token.length < 1 || interest_token.length < 1) )
+else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && ( channel_token.length < 1 || interest_token.length < 1) )
{
System.out.println( "Error: Multi Channel selected but only one setting in channels or reg_interest_points_channel" );
}
-
+
// Assembles string for Multi Channel registration
-else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length > 1 )
+else if (reg_process_channel.equalsIgnoreCase( "All channels" ) && channel_token.length > 1 )
{
for (int channel=0; channel < channel_token.length; channel++ )
- {
+ {
String channel_part = "interest_points_channel_" + channel_token[channel] + "=" + interest_token[channel] + " ";
reg_multi_channel_string.append( channel_part );
reg_multi_channel_string.append(" ");
@@ -248,15 +392,15 @@ else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List
{
System.out.println( "Error: Multi Channel one Channel contains beads selected but only one setting in channls or reg_interest_points_channel" );
}
-
+
// Assembles string for Multi Channel Processing one Channel Contains the beads
-else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && channel_token.length > 1 && interest_token.length > 1)
+else if (reg_process_channel.equalsIgnoreCase( "Single channel (Select from List)" ) && channel_token.length > 1 && interest_token.length > 1)
{
for (int channel=0; channel < channel_token.length; channel++ )
- {
+ {
String channel_part = "interest_points_channel_" + channel_token[channel] + "=" + interest_token[channel] + " ";
reg_multi_channel_string.append( channel_part );
- reg_multi_channel_string.append(" ");
+ reg_multi_channel_string.append(" ");
}
}
@@ -268,12 +412,12 @@ System.out.println( "=======================================================" );
try {
IJ.run("Toggle Cluster Processing", "display_cluster");
}
-catch ( e ) {
+catch ( e ) {
print( "[registration::activate_cluster_processing] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
-
+
}
System.out.println( "Activated Cluster Processing" );
@@ -282,38 +426,42 @@ System.out.println( "Activated Cluster Processing" );
System.out.println( "=======================================================" );
System.out.println( "Starting Detection of Interest Points" );
-System.out.println("Detect Interest Points for Registration , select_xml=" + xml_path + xml_filename + ".xml " +
+System.out.println("(Detect Interest Points for Registration , select_xml=" + xml_path + xml_filename + ".xml " +
"unique_id=" + unique_id + " " +
- "process_angle=[" + reg_process_angle + "] " +
+ "process_angle=[" + reg_process_angle + "] " +
"process_channel=[" + reg_process_channel + "] " +
- "process_illumination=[" + reg_process_illumination + "] " +
+ "process_illumination=[" + reg_process_illumination + "] " +
"process_timepoint=[" + reg_process_timepoint + "] " +
processing_channel_string +
- "xml_output=[Save every XML with user-provided unique id]" + " " +
- "processing_timepoint=[Timepoint " + parallel_timepoints + "] " +
- "type_of_interest_point_detection=[" + type_of_detection + "] " +
- "label_interest_points=" + label_interest_points + " " +
- "subpixel_localization=[" + subpixel_localization + "] " +
+ "xml_output=[Save every XML with user-provided unique id]" + " " +
+ "processing_timepoint=[Timepoint " + parallel_timepoints + "] " +
+ "type_of_interest_point_detection=[" + type_of_detection + "] " +
+ "label_interest_points=" + label_interest_points + " " +
+ "subpixel_localization=[" + subpixel_localization + "] " +
+ downsample_string +
channel_string + "" +
channel_string_multi + "" +
- "");
+ compute_string + "" +
+ ");");
try {
-IJ.run("Detect Interest Points for Registration",
- "select_xml=" + xml_path + xml_filename + ".xml " +
+IJ.run("Detect Interest Points for Registration",
+ "select_xml=" + xml_path + xml_filename + ".xml " +
"unique_id=" + unique_id + " " +
- "process_angle=[" + reg_process_angle + "] " +
+ "process_angle=[" + reg_process_angle + "] " +
"process_channel=[" + reg_process_channel + "] " +
- "process_illumination=[" + reg_process_illumination + "] " +
+ "process_illumination=[" + reg_process_illumination + "] " +
"process_timepoint=[" + reg_process_timepoint + "] " +
processing_channel_string +
- "xml_output=[Save every XML with user-provided unique id]" + " " +
- "processing_timepoint=[Timepoint " + parallel_timepoints + "] " +
- "type_of_interest_point_detection=[" + type_of_detection + "] " +
- "label_interest_points=" + label_interest_points + " " +
- "subpixel_localization=[" + subpixel_localization + "] " +
+ "xml_output=[Save every XML with user-provided unique id]" + " " +
+ "processing_timepoint=[Timepoint " + parallel_timepoints + "] " +
+ "type_of_interest_point_detection=[" + type_of_detection + "] " +
+ "label_interest_points=" + label_interest_points + " " +
+ "subpixel_localization=[" + subpixel_localization + "] " +
+ downsample_string +
channel_string + "" +
channel_string_multi + "" +
+ compute_string + "" +
"");
}
catch ( e ) {
@@ -370,12 +518,10 @@ IJ.run("Register Dataset based on Interest Points",
"allowed_error_for_ransac=" + allowed_error_for_ransac + " " +
"significance=" + significance + "");
}
-catch ( e ) {
-
+catch ( e ) {
print( "[registration::registration of interest points] caught exception: "+e );
//important to fail the process if exception occurs
runtime.exit(1);
-
}
/* shutdown */
runtime.exit(0);
diff --git a/spim_registration/timelapse/single_test.yaml b/spim_registration/timelapse/single_test.yaml
new file mode 100755
index 0000000000000000000000000000000000000000..e89c1f77f7960d3f25caad97663c72ae7d67bf2f
--- /dev/null
+++ b/spim_registration/timelapse/single_test.yaml
@@ -0,0 +1,259 @@
+common: {
+ # directory that contains the bean shell scripts and Snakefile
+ bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
+ # Directory that contains the cuda libraries
+ directory_cuda: "/sw/users/schmied/cuda/",
+ # Directory that contains the current working Fiji
+ fiji-app: "/sw/users/schmied/packages/2015-06-30_Fiji.app.cuda/ImageJ-linux64",
+ fiji-prefix: "/sw/users/schmied/packages/xvfb-run -a", # calls xvfb for Fiji headless mode
+ # xml file names without .xml suffix
+ first_xml_filename: 'single', # Name of the xml file for the .czi or .tif files
+ hdf5_xml_filename: '"hdf5_single"', # Name of .xml file for the hdf5 data after resave_hdf5
+ merged_xml: 'hdf5_single_merge', # Name of .xml file after merge
+ # Describe the dataset
+ ntimepoints: 2, # number of timepoints of dataset
+ angles: "0,72,144,216,288", # angles
+ channels: "green", # channels
+ illumination: "0", # illuminations
+ pixel_distance_x: '0.28590106964', # Manual calibration x
+ pixel_distance_y: '0.28590106964', # Manual calibration y
+ pixel_distance_z: '1.50000', # Manual calibration z
+ pixel_unit: "um", # unit of manual calibration
+ # Use switches to decide which processing steps you need:
+ # transformation_switch: "timelapse" standard processing
+ # after timelapse registration directly goes into fusion, timelapse_duplicate
+ # "timelapse_duplicate" for dual channel processing one channel contains the beads
+ # duplicates transformations
+ transformation_switch: "timelapse",
+ # Switches between content based fusion and deconvoltion
+ # "deconvolution" > for deconvolution
+ # "fusion" > for content based fusion
+ fusion_switch: "fusion"
+ }
+
+define_xml_czi: {
+ first_czi: "2015-02-21_LZ1_Stock68_3.czi", # master .czi file
+ rotation_around: "X-Axis", # axis of acquistion
+ bsh_file: "define_czi.bsh" # .bsh script for defining .czi file
+ }
+
+define_xml_tif: {
+ # file pattern of .tif files
+ # for multi channel give spim_TL{tt}_Angle{a}_Channel{c}.tif
+ # # SPIM file pattern: for padded zeros use tt
+ image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif',
+ # Settings for ImageJ Opener
+ type_of_dataset: '"Image Stacks (ImageJ Opener)"',
+ multiple_timepoints: '"YES (one file per time-point)"', # or NO (one time-point)
+ multiple_angles: '"YES (one file per angle)"', # or NO (one angle)
+ multiple_channels: '"NO (one channel)"', # or "\"NO (one channel)\""
+ multiple_illumination_directions: '"NO (one illumination direction)"', # or YES (one file per illumination direction)
+ imglib_container: '"ArrayImg (faster)"', # '"ArrayImg (faster)"'
+ bsh_file: "define_tif_zip.bsh"
+ }
+
+resave_hdf5: {
+ # Resaves .tif or .czi data into hdf5
+ # Subsampling and resolution settings for hdf5: data dependent
+ hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"',
+ subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"',
+ # Standard settings for cluster processing
+ setups_per_partition: '0',
+ timepoints_per_partition: '1',
+ resave_timepoint: '"All Timepoints"',
+ resave_angle: '"All angles"',
+ resave_channel: '"All channels"',
+ resave_illumination: '"All illuminations"',
+ bsh_file: "export.bsh"
+ }
+
+registration: {
+ # reg_process_channel:
+ # # Single Channel: '"All channels"'
+ # Dual Channel: '"All channels"'
+ # Dual Channel one Channel contains beads: '"Single channel (Select from List)"'
+ reg_process_channel: '"All channels"',
+ # reg_processing_channel:
+ # Dual Channel setting for 1 Channel contains the beads
+ reg_processing_channel: '"green"',
+ # reg_interest_points_channel:
+ # Single Channel: '"beads"'
+ # Dual Channel: '"beads,beads"'
+ # Dual Channel: Channel does not contain the beads '"[DO NOT register this channel],beads"'
+ reg_interest_points_channel: '"beads"',
+ # type of detection: '"Difference-of-Mean (Integral image based)"' or '"Difference-of-Gaussian"'
+ type_of_detection: '"Difference-of-Mean (Integral image based)"',
+ # Settings for Difference-of-Mean
+ # For multiple channels 'value1,value2' delimiter is ,
+ reg_radius_1: '2',
+ reg_radius_2: '3',
+ reg_threshold: '0.005',
+ # Settings for Difference-of-Gaussian
+ # For multiple channels 'value1,value2' delimiter is ,
+ sigma: '1.8',
+ threshold_gaussian: '0.0080',
+ # Processing setting for Difference-of-Gaussian detection
+ # compute_on:
+ compute_on: '"GPU accurate (Nvidia CUDA via JNA)"',
+ separableconvolution: '"libSeparableConvolutionCUDALib.so"',
+ # Downsampling settings
+ downsample_detection: "No", # "No" or "Yes"
+ downsample_xy: '"Match Z Resolution (less downsampling)"',
+ downsample_z: "1x",
+ # Standard Settings for bead based registration
+ label_interest_points: '"beads"',
+ reg_process_timepoint: '"Single Timepoint (Select from List)"',
+ reg_process_angle: '"All angles"',
+ reg_process_illumination: '"All illuminations"',
+ subpixel_localization: '"3-dimensional quadratic fit"',
+ detection_min_max: "find_maxima",
+ type_of_registration: '"Register timepoints individually"',
+ algorithm: '"Fast 3d geometric hashing (rotation invariant)"',
+ transformation_model: "Affine",
+ allowed_error_for_ransac: '5',
+ significance: '10',
+ fix_tiles: '"Fix first tile"',
+ map_back_tiles: '"Map back to first tile using rigid model"',
+ model_to_regularize_with: "Rigid",
+ lambda: '0.10',
+ imglib_container: '"ArrayImg (faster)"',
+ bsh_file: "registration.bsh" # .bsh script for registration
+ }
+
+xml_merge: {
+ bsh_file: "xml_merge.bsh"
+ }
+
+timelapse: {
+ reference_timepoint: '0', # Reference timepoint
+ # Standard settings for timelapse registration
+ type_of_registration_timelapse: '"Match against one reference timepoint (no global optimization)"',
+ timelapse_process_timepoints: '"All Timepoints"',
+ bsh_file: "timelapse_registration.bsh"
+ }
+
+dublicate_transformations: {
+ # If dual channel processing and only one channel contains beads
+ # this allows you to dublicate the transformation for the
+ # channel that does not contain beas
+ source_dublication: "red", # source channel
+ target_dublication: "green", # target channel
+ duplicate_which_transformations: '"Replace all transformations"', # mode of dublication
+ bsh_file: "dublicate_transformations.bsh" # .bsh script for dublication
+ }
+
+fusion: {
+ # content based multiview fusion
+ # supports multi channel without new settings
+ downsample: '2', # set downsampling
+ # Cropping parameters of full resolution
+ minimal_x: '190',
+ minimal_y: '-16',
+ minimal_z: '-348',
+ maximal_x: '1019',
+ maximal_y: '1941',
+ maximal_z: '486',
+ # fused_image: '"Append to current XML Project"', does not work yet
+ process_timepoint: '"Single Timepoint (Select from List)"',
+ process_angle: '"All angles"',
+ process_channel: '"All channels"',
+ process_illumination: '"All illuminations"',
+ imglib2_container_fusion: '"ArrayImg"',
+ interpolation: '"Linear Interpolation"',
+ pixel_type: '"16-bit unsigned integer"',
+ imglib2_data_container: '"ArrayImg (faster)"',
+ process_views_in_paralell: '"All"',
+ xml_output: '"Save every XML with user-provided unique id"',
+ bsh_file: "fusion.bsh"
+ }
+
+external_transform: {
+ # Downsamples for deconvolution
+ # BUG: external transformation breaks .xml file
+ # channel setting: '"all_channels"'
+ channel_setting: '"green"',
+ transform_timepoint: '"All Timepoints"',
+ transform_angle: '"All angles"',
+ transform_channel: '"All channels"',
+ transform_illumination: '"All illuminations"',
+ apply_transformation: '"Current view transformations (appends to current transforms)"',
+ define_mode_transform: '"Matrix"',
+ # Matrix for downsampling
+ matrix_transform: '"0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0"',
+ transformation: '"Rigid"',
+ bsh_file: "transform.bsh"
+ }
+
+deconvolution: {
+ iterations: '5', # number of iterations
+ # Cropping parameters: take downsampling into account
+ minimal_x_deco: '190',
+ minimal_y_deco: '-16',
+ minimal_z_deco: '-348',
+ maximal_x_deco: '1019',
+ maximal_y_deco: '1941',
+ maximal_z_deco: '486',
+ # Channel settings for deconvolution
+ # Single Channel: '"beads"'
+ # Dual Channel: '"beads,beads"'
+ # Dual Channel one channel contains beads: '"[Same PSF as channel red],beads"'
+ detections_to_extract_psf_for_channel: '"[Same PSF as channel red],beads"',
+ # Settings for GPU or CPU processing
+ # '"CPU (Java)"' or '"GPU (Nvidia CUDA via JNA)"'
+ compute_on: '"GPU (Nvidia CUDA via JNA)"',
+ cudafourierconvolution: "libFourierConvolutionCUDALib.so", # GPU processing name of cuda library
+ # Standard settings for deconvolution
+ process_timepoint: '"Single Timepoint (Select from List)"',
+ process_angle: '"All angles"',
+ process_channel: '"All channels"',
+ process_illumination: '"All illuminations"',
+ type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"',
+ Tikhonov_parameter: '0.0006',
+ compute: '"in 512x512x512 blocks"',
+ osem_acceleration: '"1 (balanced)"',
+ psf_estimation: '"Extract from beads"',
+ psf_size_x: '19',
+ psf_size_y: '19',
+ psf_size_z: '25',
+ imglib2_container: '"ArrayImg"',
+ bsh_file: "deconvolution.bsh"
+ }
+
+hdf5_output: {
+ # writes new hdf5 dataset for fusion output: will be obsolete
+ # Naming pattern of output
+ # Single Channel: TP{{t}}_Chgreen_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
+ # Dual Channel: TP{{t}}_Ch{{0}}_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
+ output_image_file_pattern: '"TP{{t}}_Chgreen_Ill0_Ang0,72,144,216,288.tif"',
+ # channel setting
+ output_multiple_channels: '"NO (one channel)"', # '"YES (one file per channel)"' or '"NO (one channel)"'
+ output_channels: "green",
+ # .xml file names
+ output_xml: '"fused_Single"',
+ output_hdf5_xml: '"hdf5_fused_Single"',
+ output_timepoints: '0-1', # Timepoints format: '1-2'
+ # pixel size of output: take downsampling into account!
+ output_pixel_distance_x: 0.28590106964,
+ output_pixel_distance_y: 0.28590106964,
+ output_pixel_distance_z: 0.28590106964,
+ output_pixel_unit: 'um',
+ # give if 16Bit data or 32Bit data
+ # output of fusion is 16Bit, of deconvolution it is 32Bit
+ output_data_type: "16Bit", # "32Bit" or "16Bit"
+ # if data is 32Bit then the data is converted into 16Bit data
+ convert_32bit: '"[Use min/max of first image (might saturate intenities over time)]"',
+ # subsampling and chunk size settings: dataset dependent
+ subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}}, {{4,4,4}}, {{8,8,8}} }}"', # data dependent
+ chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}}, {{16,16,16}}, {{16,16,16}} }}"', # data dependent
+ # subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}} }}"',
+ # chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}} }}"',
+ # Standard settings for hdf5_output
+ output_type_of_dataset: '"Image Stacks (ImageJ Opener)"',
+ output_multiple_timepoints: '"YES (one file per time-point)"',
+ output_multiple_angles: '"NO (one angle)"',
+ output_illumination_directions: '"NO (one illumination direction)"',
+ output_imglib_container: '"ArrayImg (faster)"',
+ bsh_file_define: "define_output.bsh", # .bsh script for defining the dataset
+ bsh_file_hdf5: "export_output.bsh" # .bsh script for resaving into hdf5
+ }
+
diff --git a/spim_registration/timelapse/tomancak.json b/spim_registration/timelapse/tomancak.json
deleted file mode 100644
index 021578435e6439631f55fdcb0780d5de97888993..0000000000000000000000000000000000000000
--- a/spim_registration/timelapse/tomancak.json
+++ /dev/null
@@ -1,88 +0,0 @@
-{
- "common" :
- {
- "fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
- "fiji-prefix" : "/sw/bin/xvfb-run -a",
- "directory_cuda" : "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
- "merged_xml" : "hdf5_test_unicore_merge"
- },
-
- "registration" :
- {
- "timepoint" : "\"Single Timepoint (Select from List)\"",
- "illuminations" : "\"All illuminations\"",
- "angle" : "\"All angles\"",
- "channel" : "\"All channels\"",
- "proc-ch" : "\"channel 1\"",
- "algorithm" : "\"Fast 3d geometric hashing (rotation invariant)\"",
- "label_interest_points" : "\"beads\"",
- "type_of_registration" : "\"Register timepoints individually\"",
- "type_of_registration_timelapse" : "\"Match against one reference timepoint (no global optimization)\"",
- "type_of_detection" : "\"Difference-of-Mean (Integral image based)\"" ,
- "subpixel_localization" : "\"3-dimensional quadratic fit\"",
- "imglib_container" : "\"ArrayImg (faster)\"",
- "radius_1" : "2",
- "radius_2" : "3",
- "threshold" : "0.005",
- "interest_points_channel_0" : "\"[DO NOT register this channel]\"" ,
- "interest_points_channel_1" : "\"beads\"",
- "fix_tiles" : "\"Fix first tile\"" ,
- "map_back_tiles" : "\"Map back to first tile using rigid model\"",
- "transformation_model" : "Affine",
- "model_to_regularize_with" : "Rigid",
- "lambda" : "0.10" ,
- "allowed_error_for_ransac" : "5",
- "detection_min_max" : "find_maxima",
- "initial_sigma" : "1.8",
- "threshold_gaussian" : "0.0080",
- "bsh_file" : "registration.bsh"
- },
-
- "xml_merge" :
- {
- "bsh_file" : "xml_merge.bsh"
- },
-
- "external_transform" :
- {
- "bsh_file" : "transform.bsh",
- "angle" : "\"All angles\"",
- "channel" : "\"All channels\"",
- "illumination" : "\"All illuminations\"",
- "timepoint" : "\"All Timepoints\"",
- "transformation" : "\"Rigid\"",
- "apply_transformation" : "\"Current view transformations (appends to current transforms)\"",
- "define_mode_transform" : "\"Matrix\"",
- "matrix_transform" : "\"0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0\""
- },
-
- "deconvolution" :
- {
-
- "bsh_file" : "deconvolution_GPU.bsh",
- "process_timepoint" : "\"Single Timepoint (Select from List)\"",
- "process_channel" : "\"All channels\"",
- "process_illumination" : "\"All illuminations\"",
- "process_angle" : "\"All angles\"",
- "minimal_x" : "76",
- "minimal_y" : "4",
- "minimal_z" : "-192",
- "maximal_x" : "488",
- "maximal_y" : "956",
- "maximal_z" : "214",
- "imglib2_container" : "\"ArrayImg \"",
- "type_of_iteration" : "\"Efficient Bayesian - Optimization I (fast, precise)\"",
- "osem_acceleration" : "\"1 (balanced)\"",
- "Tikhonov_parameter" : "0.0006",
- "compute" : "\"in 512x512x512 blocks\"",
- "compute_on" : "\"GPU (Nvidia CUDA via JNA)\"",
- "psf_estimation" : "\"Extract from beads\"",
- "iterations" : "5",
- "detections_to_extract_psf_for_channel_0" : "\"beads\"",
- "detections_to_extract_psf_for_channel_1" : "\"beads\"",
- "psf_size_x" : "19",
- "psf_size_y" : "19",
- "psf_size_z" : "25"
- }
-
-}
diff --git a/spim_registration/timelapse/tomancak_czi.json b/spim_registration/timelapse/tomancak_czi.json
deleted file mode 100644
index 9a2445f03860cec92dec550035d55edcc38ada2e..0000000000000000000000000000000000000000
--- a/spim_registration/timelapse/tomancak_czi.json
+++ /dev/null
@@ -1,204 +0,0 @@
-{
- "common" :
- {
- "fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
- "fiji-prefix" : "/sw/bin/xvfb-run -a",
- "directory_cuda" : "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
- "merged_xml" : "hdf5_test_unicore_merge",
- "bsh_directory" : "/home/steinbac/development/cschmied-snakemake-workflows/spim_registration/timelapse/",
- "first_xml_filename" : "test_unicore",
- "hdf5_xml_filename" : "\"hdf5_test_unicore\"",
- "fusion_switch" : "deconvolution",
- "ntimepoints" : 3
- },
-
- "define_xml_czi" :
- {
- "pixel_distance_x" : "0.2875535786151886",
- "pixel_distance_y" : "0.2875535786151886",
- "pixel_distance_z" : "1.50000",
- "pixel_unit" : "um",
- "first_czi" : "2015-02-21_LZ1_Stock68_3.czi",
- "channel_1" : "green",
- "channel_2" : "red",
- "angle_1" : "0",
- "angle_2" : "72",
- "angle_3" :"144",
- "angle_4" :"216",
- "angle_5" : "288",
- "illumination_1" : "0",
- "rotation_around" : "X-Axis",
- "bsh_file" : "define_czi.bsh"
- },
-
- "define_xml_tif" :
- {
- "timepoints" : "0-1",
- "acquisition_angles" : "0,72,144,216,288",
- "channels" : "0",
- "image_file_pattern" : "img_TL{{t}}_Angle{{a}}.tif",
- "pixel_distance_x" : "0.2875535786151886",
- "pixel_distance_y" : "0.2875535786151886",
- "pixel_distance_z" : "1.50000",
- "pixel_unit" : "um",
- "multiple_timepoints" : "\"YES (one file per time-point)\"",
- "multiple_channels" : "\"NO (one channel)\"",
- "multiple_illumination_directions" : "\"NO (one illumination direction)\"",
- "multiple_angles" : "\"YES (one file per angle)\"",
- "type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
- "imglib_container" : "\"ArrayImg (faster)\"",
- "bsh_file" : "define_tif_zip.bsh"
- },
-
- "resave_hdf5" :
- {
- "parallel_timepoints" : "3",
- "resave_angle" : "\"All angles\"",
- "resave_channel" : "\"All channels\"",
- "resave_illumination" : "\"All illuminations\"",
- "resave_timepoint" : "\"All Timepoints\"",
- "subsampling_factors" : "\"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}\"",
- "hdf5_chunk_sizes" : "\"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}\"",
- "timepoints_per_partition" : "1",
- "setups_per_partition" : "0",
- "bsh_file" : "export.bsh"
- },
-
- "registration" :
- {
- "timepoint" : "\"Single Timepoint (Select from List)\"",
- "illuminations" : "\"All illuminations\"",
- "angle" : "\"All angles\"",
- "channel" : "\"All channels\"",
- "proc-ch" : "\"channel 0\"",
- "algorithm" : "\"Fast 3d geometric hashing (rotation invariant)\"",
- "label_interest_points" : "\"beads\"",
- "type_of_registration" : "\"Register timepoints individually\"",
- "type_of_detection" : "\"Difference-of-Mean (Integral image based)\"" ,
- "subpixel_localization" : "\"3-dimensional quadratic fit\"",
- "imglib_container" : "\"ArrayImg (faster)\"",
- "radius_1" : "2",
- "radius_2" : "3",
- "threshold" : "0.005",
- "interest_points_channel_0" : "\"beads\"",
- "interest_points_channel_1" : "\"beads\"",
- "fix_tiles" : "\"Fix first tile\"",
- "map_back_tiles" : "\"Map back to first tile using rigid model\"",
- "transformation_model" : "Affine",
- "model_to_regularize_with" : "Rigid",
- "lambda" : "0.10" ,
- "allowed_error_for_ransac" : "5",
- "significance" : "10",
- "detection_min_max" : "find_maxima",
- "initial_sigma" : "1.8",
- "threshold_gaussian" : "0.0080",
- "bsh_file" : "registration.bsh"
- },
-
- "xml_merge" :
- {
- "bsh_file" : "xml_merge.bsh"
- },
-
- "timelapse" :
- {
- "reference_timepoint" : "0",
- "timelapse_process_timepoints" : "\"All Timepoints\"",
- "type_of_registration_timelapse" : "\"Match against one reference timepoint (no global optimization)\"",
- "bsh_file" : "timelapse_registration.bsh"
- },
-
- "external_transform" :
- {
- "bsh_file" : "transform.bsh",
- "angle" : "\"All angles\"",
- "channel" : "\"All channels\"",
- "illumination" : "\"All illuminations\"",
- "timepoint" : "\"All Timepoints\"",
- "transformation" : "\"Rigid\"",
- "apply_transformation" : "\"Current view transformations (appends to current transforms)\"",
- "define_mode_transform" : "\"Matrix\"",
- "matrix_transform" : "\"0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0\""
- },
-
- "fusion" :
- {
- "minimal_x" : "128",
- "minimal_y" : "-13",
- "minimal_z" : "-407",
- "maximal_x" : "986",
- "maximal_y" : "1927",
- "maximal_z" : "498",
- "downsample" : "1",
- "process_timepoint" : "\"Single Timepoint (Select from List)\"",
- "process_channel" : "\"All channels\"",
- "process_illumination" : "\"All illuminations\"",
- "process_angle" : "\"All angles\"",
- "xml_output" : "\"Save every XML with user-provided unique id\"",
- "fused_image" : "\"Append to current XML Project\"",
- "pixel_type" : "\"16-bit unsigned integer\"",
- "imglib2_container_fusion" : "\"ArrayImg\"",
- "process_views_in_paralell" : "\"All\"",
- "interpolation" : "\"Linear Interpolation\"",
- "imglib2_data_container" : "\"ArrayImg (faster)\"",
- "bsh_file" : "fusion.bsh"
- },
-
- "deconvolution" :
- {
-
- "bsh_file" : "deconvolution_GPU.bsh",
- "process_timepoint" : "\"Single Timepoint (Select from List)\"",
- "process_channel" : "\"All channels\"",
- "process_illumination" : "\"All illuminations\"",
- "process_angle" : "\"All angles\"",
- "minimal_x" : "76",
- "minimal_y" : "4",
- "minimal_z" : "-192",
- "maximal_x" : "488",
- "maximal_y" : "956",
- "maximal_z" : "214",
- "imglib2_container" : "\"ArrayImg \"",
- "type_of_iteration" : "\"Efficient Bayesian - Optimization I (fast, precise)\"",
- "osem_acceleration" : "\"1 (balanced)\"",
- "Tikhonov_parameter" : "0.0006",
- "compute" : "\"in 512x512x512 blocks\"",
- "compute_on" : "\"GPU (Nvidia CUDA via JNA)\"",
- "psf_estimation" : "\"Extract from beads\"",
- "iterations" : "5",
- "detections_to_extract_psf_for_channel_0" : "\"beads\"",
- "detections_to_extract_psf_for_channel_1" : "\"beads\"",
- "psf_size_x" : "19",
- "psf_size_y" : "19",
- "psf_size_z" : "25"
- },
-
- "hdf5_output" :
- {
- "output_image_file_pattern" : "TP{{t}}_Ch{{c}}_Ill0_Ang0,72,144,216,288.tif",
- "output_data_type" : "32Bit",
- "output_xml" : "\"fused_Dual_Channel\"",
- "output_hdf5_xml" : "\"hdf5_fused_Stock68\"",
- "output_multiple_channels" : "\"NO (one channel)\"",
- "output_timepoints" : "0-1",
- "output_channels" : "green",
- "output_pixel_distance_x" : "0.5718",
- "output_pixel_distance_y" : "0.5718",
- "output_pixel_distance_z" : "0.5718",
- "output_pixel_unit" : "um",
- "output_multiple_timepoints" : "\"YES (one file per time-point)\"",
- "output_illumination_directions" : "\"NO (one illumination direction)\"",
- "output_multiple_angles" : "\"NO (one angle)\"",
- "output_type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
- "output_imglib_container" : "\"ArrayImg (faster)\"",
- "bsh_file_define" : "/define_output.bsh",
- "bsh_file_hdf5" : "/export_output.bsh",
- "convert_32bit" : "\"[Use min/max of first image (might saturate intenities over time)]\""
-
- }
-
-
-
-
-
-}
diff --git a/spim_registration/timelapse/tomancak_test_cluster.json b/spim_registration/timelapse/tomancak_test_cluster.json
deleted file mode 100644
index 44899c53b1b4dca63946a6b2a9d852faa25c9909..0000000000000000000000000000000000000000
--- a/spim_registration/timelapse/tomancak_test_cluster.json
+++ /dev/null
@@ -1,202 +0,0 @@
-{
- "common" :
- {
- "fiji-app" : "/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/ImageJ-linux64",
- "fiji-prefix" : "/sw/bin/xvfb-run -a",
- "directory_cuda" : "/lustre/projects/hpcsupport/steinbac/unicore/christopher/unicore_jobs/Fiji.app.cuda_new/lib/",
- "merged_xml" : "hdf5_test_unicore_merge",
- "bsh_directory" : "/home/steinbac/development/schmied-snakemake-workflows/spim_registration/timelapse/",
- "first_xml_filename" : "test_unicore",
- "hdf5_xml_filename" : "\"hdf5_test_unicore\"",
- "fusion_switch" : "deconvolution",
- "ntimepoints" : 5
- },
-
- "define_xml_czi" :
- {
- "pixel_distance_x" : "0.28590106964",
- "pixel_distance_y" : "0.28590106964",
- "pixel_distance_z" : "1.50000",
- "pixel_unit" : "um",
- "first_czi" : "2015-04-11_LZ2_Stock68_3.czi",
- "channel_1" : "green",
- "channel_2" : "red",
- "angle_1" : "0",
- "angle_2" : "72",
- "angle_3" : "144",
- "angle_4" : "216",
- "angle_5" : "288",
- "illumination_1" : "0",
- "rotation_around" : "X-Axis",
- "bsh_file" : "define_czi.bsh"
- },
-
- "define_xml_tif" :
- {
- "acquisition_angles" : "0,72,144,216,288",
- "channels" : "0",
- "image_file_pattern" : "img_TL{{t}}_Angle{{a}}.tif",
- "pixel_distance_x" : "0.28590106964",
- "pixel_distance_y" : "0.28590106964",
- "pixel_distance_z" : "1.50000",
- "pixel_unit" : "um",
- "multiple_timepoints" : "\"YES (one file per time-point)\"",
- "multiple_channels" : "\"NO (one channel)\"",
- "multiple_illumination_directions" : "\"NO (one illumination direction)\"",
- "multiple_angles" : "\"YES (one file per angle)\"",
- "type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
- "imglib_container" : "\"ArrayImg (faster)\"",
- "bsh_file" : "define_tif_zip.bsh"
- },
-
- "resave_hdf5" :
- {
- "resave_angle" : "\"All angles\"",
- "resave_channel" : "\"All channels\"",
- "resave_illumination" : "\"All illuminations\"",
- "resave_timepoint" : "\"All Timepoints\"",
- "subsampling_factors" : "\"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}\"",
- "hdf5_chunk_sizes" : "\"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}\"",
- "timepoints_per_partition" : "1",
- "setups_per_partition" : "0",
- "bsh_file" : "export.bsh"
- },
-
- "registration" :
- {
- "timepoint" : "\"Single Timepoint (Select from List)\"",
- "illuminations" : "\"All illuminations\"",
- "angle" : "\"All angles\"",
- "channel" : "\"All channels\"",
- "proc-ch" : "\"channel 0\"",
- "algorithm" : "\"Fast 3d geometric hashing (rotation invariant)\"",
- "label_interest_points" : "\"beads\"",
- "type_of_registration" : "\"Register timepoints individually\"",
- "type_of_detection" : "\"Difference-of-Mean (Integral image based)\"" ,
- "subpixel_localization" : "\"3-dimensional quadratic fit\"",
- "imglib_container" : "\"ArrayImg (faster)\"",
- "radius_1" : "2",
- "radius_2" : "3",
- "threshold" : "0.005",
- "interest_points_channel_0" : "\"beads\"",
- "interest_points_channel_1" : "\"beads\"",
- "fix_tiles" : "\"Fix first tile\"",
- "map_back_tiles" : "\"Map back to first tile using rigid model\"",
- "transformation_model" : "Affine",
- "model_to_regularize_with" : "Rigid",
- "lambda" : "0.10" ,
- "allowed_error_for_ransac" : "5",
- "significance" : "10",
- "detection_min_max" : "find_maxima",
- "initial_sigma" : "1.8",
- "threshold_gaussian" : "0.0080",
- "bsh_file" : "registration.bsh"
- },
-
- "xml_merge" :
- {
- "bsh_file" : "xml_merge.bsh"
- },
-
- "timelapse" :
- {
- "reference_timepoint" : "0",
- "timelapse_process_timepoints" : "\"All Timepoints\"",
- "type_of_registration_timelapse" : "\"Match against one reference timepoint (no global optimization)\"",
- "bsh_file" : "timelapse_registration.bsh"
- },
-
- "external_transform" :
- {
- "bsh_file" : "transform.bsh",
- "angle" : "\"All angles\"",
- "channel" : "\"All channels\"",
- "illumination" : "\"All illuminations\"",
- "timepoint" : "\"All Timepoints\"",
- "transformation" : "\"Rigid\"",
- "apply_transformation" : "\"Current view transformations (appends to current transforms)\"",
- "define_mode_transform" : "\"Matrix\"",
- "matrix_transform" : "\"0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0\""
- },
-
- "fusion" :
- {
- "minimal_x" : "190",
- "minimal_y" : "-16",
- "minimal_z" : "-348",
- "maximal_x" : "1019",
- "maximal_y" : "1941",
- "maximal_z" : "486",
- "downsample" : "1",
- "process_timepoint" : "\"Single Timepoint (Select from List)\"",
- "process_channel" : "\"All channels\"",
- "process_illumination" : "\"All illuminations\"",
- "process_angle" : "\"All angles\"",
- "xml_output" : "\"Save every XML with user-provided unique id\"",
- "fused_image" : "\"Append to current XML Project\"",
- "pixel_type" : "\"16-bit unsigned integer\"",
- "imglib2_container_fusion" : "\"ArrayImg\"",
- "process_views_in_paralell" : "\"All\"",
- "interpolation" : "\"Linear Interpolation\"",
- "imglib2_data_container" : "\"ArrayImg (faster)\"",
- "bsh_file" : "fusion.bsh"
- },
-
- "deconvolution" :
- {
-
- "bsh_file" : "deconvolution_GPU.bsh",
- "process_timepoint" : "\"Single Timepoint (Select from List)\"",
- "process_channel" : "\"All channels\"",
- "process_illumination" : "\"All illuminations\"",
- "process_angle" : "\"All angles\"",
- "minimal_x" : "95",
- "minimal_y" : "-8",
- "minimal_z" : "-174",
- "maximal_x" : "509",
- "maximal_y" : "970",
- "maximal_z" : "243",
- "imglib2_container" : "\"ArrayImg \"",
- "type_of_iteration" : "\"Efficient Bayesian - Optimization I (fast, precise)\"",
- "osem_acceleration" : "\"1 (balanced)\"",
- "Tikhonov_parameter" : "0.0006",
- "compute" : "\"in 512x512x512 blocks\"",
- "compute_on" : "\"GPU (Nvidia CUDA via JNA)\"",
- "psf_estimation" : "\"Extract from beads\"",
- "iterations" : "5",
- "detections_to_extract_psf_for_channel_0" : "\"beads\"",
- "detections_to_extract_psf_for_channel_1" : "\"beads\"",
- "psf_size_x" : "19",
- "psf_size_y" : "19",
- "psf_size_z" : "25"
- },
-
- "hdf5_output" :
- {
- "output_image_file_pattern" : "TP{{t}}_Ch{{c}}_Ill0_Ang0,72,144,216,288.tif",
- "output_data_type" : "32Bit",
- "output_xml" : "\"fused_Dual_Channel\"",
- "output_hdf5_xml" : "\"hdf5_fused_Stock68\"",
- "output_multiple_channels" : "\"NO (one channel)\"",
- "output_timepoints" : "0-4",
- "output_channels" : "green",
- "output_pixel_distance_x" : "0.5718",
- "output_pixel_distance_y" : "0.5718",
- "output_pixel_distance_z" : "0.5718",
- "output_pixel_unit" : "um",
- "output_multiple_timepoints" : "\"YES (one file per time-point)\"",
- "output_illumination_directions" : "\"NO (one illumination direction)\"",
- "output_multiple_angles" : "\"NO (one angle)\"",
- "output_type_of_dataset" : "\"Image Stacks (ImageJ Opener)\"",
- "output_imglib_container" : "\"ArrayImg (faster)\"",
- "bsh_file_define" : "/define_output.bsh",
- "bsh_file_hdf5" : "/export_output.bsh",
- "convert_32bit" : "\"[Use min/max of first image (might saturate intenities over time)]\""
-
- }
-
-
-
-
-
-}
diff --git a/spim_registration/timelapse/tomancak_test_cluster.yaml b/spim_registration/timelapse/tomancak_test_cluster.yaml
index 84c42f55c8998a77e4113a35bc62b4f52be471e7..b0095960b0242d6a250f8854b9e2866500793375 100755
--- a/spim_registration/timelapse/tomancak_test_cluster.yaml
+++ b/spim_registration/timelapse/tomancak_test_cluster.yaml
@@ -1,66 +1,108 @@
common: {
- # directory that contains the bean shell scripts
- bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
- directory_cuda: "/sw/users/schmied/packages/cuda/lib/",
- fiji-app: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/ImageJ-linux64",
- fiji-prefix: "/sw/bin/xvfb-run -a",
- first_xml_filename: "Dual_Channel",
- hdf5_xml_filename: '"hdf5_Dual_Channel"',
- merged_xml: "hdf5_Dual_Channel_merge",
- ntimepoints: 2,
- angles: "0,72,144,216,288",
- channels: "green,red",
- illumination: "0",
- pixel_distance_x: '0.28590',
- pixel_distance_y: '0.28590',
- pixel_distance_z: '1.50000',
- pixel_unit: "um",
- transformation_switch: "timelapse_dublicate",
- # transformation_switch: "timelapse",
- # fusion_switch: "deconvolution"
- fusion_switch: "fusion"
+ # directory that contains the bean shell scripts and Snakefile
+ bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
+ # Directory that contains the cuda libraries
+ directory_cuda: "/sw/users/schmied/cuda/",
+ # Directory that contains the current working Fiji
+ #fiji-app: "/sw/users/schmied/packages/2015-06-08_Fiji.app.cuda/ImageJ-linux64",
+ fiji-app: "/sw/users/schmied/packages/2015-05-29_Fiji_2.3.9_SNAP.app.cuda/ImageJ-linux64",
+ fiji-prefix: "/sw/bin/xvfb-run -a", # calls xvfb for Fiji headless mode
+ # xml file names without .xml suffix
+ first_xml_filename: "Dual_Channel", # Name of the xml file for the .czi or .tif files
+ hdf5_xml_filename: '"hdf5_Dual_Channel"', # Name of .xml file for the hdf5 data after resave_hdf5
+ merged_xml: "hdf5_Dual_Channel_merge", # Name of .xml file after merge
+ # Describe the dataset
+ ntimepoints: 2, # number of timepoints of dataset
+ angles: "0,72,144,216,288", # angles
+ channels: "green,red", # channels
+ illumination: "0", # illuminations
+ pixel_distance_x: '0.28590', # Manual calibration x
+ pixel_distance_y: '0.28590', # Manual calibration y
+ pixel_distance_z: '1.50000', # Manual calibration z
+ pixel_unit: "um", # unit of manual calibration
+ # Use switches to decide which processing steps you need:
+ # transformation_switch: "timelapse" standard processing
+ # after timelapse registration directly goes into fusion, timelapse_duplicate
+ # "timelapse_duplicate" for dual channel processing one channel contains the beads
+ # duplicates transformations
+ transformation_switch: "timelapse_duplicate",
+ # Switches between content based fusion and deconvoltion
+ # "deconvolution" > for deconvolution
+ # "fusion" > for content based fusion
+ fusion_switch: "deconvolution"
}
-
+
define_xml_czi: {
- first_czi: "2015-02-20_LZ2_Stock48_Stock58.czi", # essential
- rotation_around: "X-Axis",
- bsh_file: "define_czi.bsh"
+ first_czi: "2015-02-20_LZ2_Stock48_Stock58.czi", # master .czi file
+ rotation_around: "X-Axis", # axis of acquistion
+ bsh_file: "define_czi.bsh" # .bsh script for defining .czi file
}
define_xml_tif: {
- image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif', # essential
- imglib_container: '"ArrayImg (faster)"',
- multiple_angles: '"YES (one file per angle)"',
- multiple_channels: '"NO (one channel)"',
- multiple_illumination_directions: '"NO (one illumination direction)"',
- multiple_timepoints: '"YES (one file per time-point)"',
+ # file pattern of .tif files
+ # for multi channel give spim_TL{tt}_Angle{a}_Channel{c}.tif
+ # # SPIM file pattern: for padded zeros use tt
+ image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif',
+ # Settings for ImageJ Opener
type_of_dataset: '"Image Stacks (ImageJ Opener)"',
- bsh_file: "define_tif_zip.bsh"
+ multiple_timepoints: '"YES (one file per time-point)"', # or NO (one time-point)
+ multiple_angles: '"YES (one file per angle)"', # or NO (one angle)
+ multiple_channels: '"NO (one channel)"', # or "\"NO (one channel)\""
+ multiple_illumination_directions: '"NO (one illumination direction)"', # or YES (one file per illumination direction)
+ imglib_container: '"ArrayImg (faster)"', # '"ArrayImg (faster)"'
+ bsh_file: "define_tif_zip.bsh"
}
resave_hdf5: {
- hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"', # data dependent
- subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"', # data dependent
+ # Resaves .tif or .czi data into hdf5
+ # Subsampling and resolution settings for hdf5: data dependent
+ hdf5_chunk_sizes: '"{{ {{32,32,4}}, {{32,32,4}}, {{16,16,16}}, {{16,16,16}} }}"',
+ subsampling_factors: '"{{ {{1,1,1}}, {{2,2,1}}, {{4,4,1}}, {{8,8,1}} }}"',
+ # Standard settings for cluster processing
+ setups_per_partition: '0',
+ timepoints_per_partition: '1',
+ resave_timepoint: '"All Timepoints"',
resave_angle: '"All angles"',
resave_channel: '"All channels"',
resave_illumination: '"All illuminations"',
- resave_timepoint: '"All Timepoints"',
- setups_per_partition: '0',
- timepoints_per_partition: '1',
bsh_file: "export.bsh"
}
registration: {
- reg_process_channel: '"Single channel (Select from List)"', # essential '"All channels"'; '"Single channel (Select from List)"'
- reg_processing_channel: '"red"', # essential
- reg_interest_points_channel: '"beads"', # essential
- reg_radius_1: '2', # essential
- reg_radius_2: '3', # essential
- reg_threshold: '0.005', # essential
- initial_sigma: '1.8', # essetial
- threshold_gaussian: '0.0080', # essential
- type_of_detection: '"Difference-of-Mean (Integral image based)"', # switch
- label_interest_points: '"beads"',
+ # reg_process_channel:
+ # # Single Channel: '"All channels"'
+ # Dual Channel: '"All channels"'
+ # Dual Channel one Channel contains beads: '"Single channel (Select from List)"'
+ reg_process_channel: '"Single channel (Select from List)"',
+ # reg_processing_channel:
+ # Dual Channel setting for 1 Channel contains the beads
+ reg_processing_channel: '"red"',
+ # reg_interest_points_channel:
+ # Single Channel: '"beads"'
+ # Dual Channel: '"beads,beads"'
+ # Dual Channel: Channel does not contain the beads '"[DO NOT register this channel],beads"'
+ reg_interest_points_channel: '"beads"',
+ # type of detection: '"Difference-of-Mean (Integral image based)"' or '"Difference-of-Gaussian"'
+ type_of_detection: '"Difference-of-Mean (Integral image based)"',
+ # Settings for Difference-of-Mean
+ # For multiple channels 'value1,value2' delimiter is ,
+ reg_radius_1: '2',
+ reg_radius_2: '3',
+ reg_threshold: '0.005',
+ # Settings for Difference-of-Gaussian
+ # For multiple channels 'value1,value2' delimiter is ,
+ sigma: '1.8',
+ threshold_gaussian: '0.0080',
+ # Processing setting for Difference-of-Gaussian detection
+ # compute_on:
+ compute_on: '"GPU accurate (Nvidia CUDA via JNA)"',
+ separableconvolution: '"libSeparableConvolutionCUDALib.so"',
+ # Downsampling settings
+ downsample_detection: "No", # "No" or "Yes"
+ downsample_xy: '"Match Z Resolution (less downsampling)"',
+ downsample_z: "1x",
+ # Standard Settings for bead based registration
+ label_interest_points: '"beads"',
reg_process_timepoint: '"Single Timepoint (Select from List)"',
reg_process_angle: '"All angles"',
reg_process_illumination: '"All illuminations"',
@@ -76,7 +118,7 @@ registration: {
model_to_regularize_with: "Rigid",
lambda: '0.10',
imglib_container: '"ArrayImg (faster)"',
- bsh_file: "registration.bsh"
+ bsh_file: "registration.bsh" # .bsh script for registration
}
xml_merge: {
@@ -84,107 +126,135 @@ xml_merge: {
}
timelapse: {
- reference_timepoint: '0', # essential
+ reference_timepoint: '0', # Reference timepoint
+ # Standard settings for timelapse registration
type_of_registration_timelapse: '"Match against one reference timepoint (no global optimization)"',
timelapse_process_timepoints: '"All Timepoints"',
bsh_file: "timelapse_registration.bsh"
}
dublicate_transformations: {
- source_dublication: "red", # essential for 1 usecase
- target_dublication: "green", # essential for 1 usecase
- duplicate_which_transformations: '"Replace all transformations"',
- bsh_file: "dublicate_transformations.bsh"
+ # If dual channel processing and only one channel contains beads
+ # this allows you to dublicate the transformation for the
+ # channel that does not contain beas
+ source_dublication: "red", # source channel
+ target_dublication: "green", # target channel
+ duplicate_which_transformations: '"Replace all transformations"', # mode of dublication
+ bsh_file: "dublicate_transformations.bsh" # .bsh script for dublication
}
fusion: {
- downsample: '1', # essential
- minimal_x: '220', # essential maybe automate
- minimal_y: '40', # essential maybe automate
- minimal_z: '-290', # essential maybe automate
- maximal_x: '976', # essential maybe automate
- maximal_y: '1892', # essential maybe automate
- maximal_z: '472', # essential maybe automate
- fused_image: '"Append to current XML Project"',
- imglib2_container_fusion: '"ArrayImg"',
- imglib2_data_container: '"ArrayImg (faster)"',
- interpolation: '"Linear Interpolation"',
- pixel_type: '"16-bit unsigned integer"',
+ # content based multiview fusion
+ # supports multi channel without new settings
+ downsample: '1', # set downsampling
+ # Cropping parameters of full resolution
+ minimal_x: '220',
+ minimal_y: '40',
+ minimal_z: '-290',
+ maximal_x: '976',
+ maximal_y: '1892',
+ maximal_z: '472',
+ # fused_image: '"Append to current XML Project"', does not work yet
+ process_timepoint: '"Single Timepoint (Select from List)"',
process_angle: '"All angles"',
process_channel: '"All channels"',
process_illumination: '"All illuminations"',
- process_timepoint: '"Single Timepoint (Select from List)"',
+ imglib2_container_fusion: '"ArrayImg"',
+ interpolation: '"Linear Interpolation"',
+ pixel_type: '"16-bit unsigned integer"',
+ imglib2_data_container: '"ArrayImg (faster)"',
process_views_in_paralell: '"All"',
xml_output: '"Save every XML with user-provided unique id"',
bsh_file: "fusion.bsh"
}
external_transform: {
- # BUG
+ # Downsamples for deconvolution
+ # BUG: external transformation breaks .xml file
# channel setting: '"all_channels"'
channel_setting: '"green,red"',
transform_timepoint: '"All Timepoints"',
transform_angle: '"All angles"',
transform_channel: '"All channels"',
- # illumination setting only one illumination side
transform_illumination: '"All illuminations"',
apply_transformation: '"Current view transformations (appends to current transforms)"',
define_mode_transform: '"Matrix"',
- matrix_transform: '"0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0"', # essential
+ # Matrix for downsampling
+ matrix_transform: '"0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0"',
transformation: '"Rigid"',
bsh_file: "transform.bsh"
}
deconvolution: {
- iterations: '1', # essential
- minimal_x_deco: '190', # essential maybe automate
- minimal_y_deco: '-16', # essential maybe automate
- minimal_z_deco: '-348', # essential maybe automate
- maximal_x_deco: '1019', # essential maybe automate
- maximal_y_deco: '1941', # essential maybe automate
- maximal_z_deco: '486', # essential maybe automate
- detections_to_extract_psf_for_channel: '"beads"',
+ iterations: '1', # number of iterations
+ # Cropping parameters: take downsampling into account
+ minimal_x_deco: '190',
+ minimal_y_deco: '-16',
+ minimal_z_deco: '-348',
+ maximal_x_deco: '1019',
+ maximal_y_deco: '1941',
+ maximal_z_deco: '486',
+ # Channel settings for deconvolution
+ # Single Channel: '"beads"'
+ # Dual Channel: '"beads,beads"'
+ # Dual Channel one channel contains beads: '"[Same PSF as channel red],beads"'
+ detections_to_extract_psf_for_channel: '"[Same PSF as channel red],beads"',
+ # Settings for GPU or CPU processing
+ # '"CPU (Java)"' or '"GPU (Nvidia CUDA via JNA)"'
+ compute_on: '"GPU (Nvidia CUDA via JNA)"',
+ cudafourierconvolution: "libFourierConvolutionCUDALib.so", # GPU processing name of cuda library
+ # Standard settings for deconvolution
process_timepoint: '"Single Timepoint (Select from List)"',
process_angle: '"All angles"',
process_channel: '"All channels"',
process_illumination: '"All illuminations"',
+ type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"',
Tikhonov_parameter: '0.0006',
compute: '"in 512x512x512 blocks"',
- compute_on: '"GPU (Nvidia CUDA via JNA)"',
- imglib2_container: '"ArrayImg"',
osem_acceleration: '"1 (balanced)"',
psf_estimation: '"Extract from beads"',
psf_size_x: '19',
psf_size_y: '19',
psf_size_z: '25',
- type_of_iteration: '"Efficient Bayesian - Optimization I (fast, precise)"',
- bsh_file: "deconvolution_GPU.bsh"
+ imglib2_container: '"ArrayImg"',
+ bsh_file: "deconvolution.bsh"
}
hdf5_output: {
- # Will be obsolete
+ # writes new hdf5 dataset for fusion output: will be obsolete
+ # Naming pattern of output
+ # Single Channel: TP{t}_Chgreen_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
+ # Dual Channel: TP{t}_Ch{0}_Ill0_Ang0,72,144,216,288.tif > Ch{name} is added here
output_image_file_pattern: 'TP{{t}}_Ch{{c}}_Ill0_Ang0,72,144,216,288.tif',
+ # channel setting
+ output_multiple_channels: '"YES (one file per channel)"', # '"YES (one file per channel)"' or '"NO (one channel)"'
+ output_channels: "green,red",
+ # .xml file names
output_xml: '"fused_Dual_Channel"',
output_hdf5_xml: '"hdf5_fused_Dual_Channel"',
- output_multiple_channels: '"YES (one file per channel)"', # "\"YES (one file per channel)\"" or "\"NO (one channel)\""
- output_timepoints: '0-1',
- output_pixel_distance_x: 0.28590,
+ output_timepoints: '0-1', # Timepoints format: '1-2'
+ # pixel size of output: take downsampling into account!
+ output_pixel_distance_x: 0.28590,
output_pixel_distance_y: 0.28590,
output_pixel_distance_z: 0.28590,
output_pixel_unit: 'um',
- output_channels: "green,red",
- output_data_type: "16Bit",
+ # give if 16Bit data or 32Bit data
+ # output of fusion is 16Bit, of deconvolution it is 32Bit
+ output_data_type: "16Bit", # "32Bit" or "16Bit"
+ # if data is 32Bit then the data is converted into 16Bit data
convert_32bit: '"[Use min/max of first image (might saturate intenities over time)]"',
+ # subsampling and chunk size settings: dataset dependent
+ subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}}, {{4,4,4}}, {{8,8,8}} }}"', # data dependent
+ chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}}, {{16,16,16}}, {{16,16,16}} }}"', # data dependent
+ # subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}} }}"',
+ # chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}} }}"',
+ # Standard settings for hdf5_output
output_type_of_dataset: '"Image Stacks (ImageJ Opener)"',
output_multiple_timepoints: '"YES (one file per time-point)"',
output_multiple_angles: '"NO (one angle)"',
output_illumination_directions: '"NO (one illumination direction)"',
output_imglib_container: '"ArrayImg (faster)"',
- subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}}, {{4,4,4}}, {{8,8,8}} }}"', # data dependent
- chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}}, {{16,16,16}}, {{16,16,16}} }}"', # data dependent
- # subsampling_output: '"{{ {{1,1,1}}, {{2,2,2}} }}"',
- # chunk_sizes_output: '"{{ {{16,16,16}}, {{16,16,16}} }}"',
- bsh_file_define: "define_output.bsh",
- bsh_file_hdf5: "export_output.bsh"
+ bsh_file_define: "define_output.bsh", # .bsh script for defining the dataset
+ bsh_file_hdf5: "export_output.bsh" # .bsh script for resaving into hdf5
}